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library(tadaA)
setwd("/storage11_7T/fuy/TADA-A")
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TADA_A_adjust_mutrate(window_file = 'db/MS_data/windows_partition/cd_windows_with_div_score.bed',
                      mut_file = '/storage11_7T/fuy/TADA-A/cell_WES/2220_mis_nlt1_pli_denovo.bed',
                      genes = "all",
                      sample_size = 6430,
                      mutrate_mode = "regular",
                      scaling_file_name = "cell_WES/cd_mis_pli_syn.2220DNM_6430fam_scaling_factors.txt",
                      scale_features = c("GC_content", "div_score"))
[1] "Made a tmp folder for tmp files."
[1] "Finished calculating mutation count within per genomic window. Time consumed: 2.734s"
[1] "Finished fitting mutation rate model and calculating scaling factors. Time consumed: 7.295s"
[1] "Removed temporary files."
A matrix: 3 × 4 of type dbl
EstimateStd. Errorz valuePr(>|z|)
(Intercept)-1.154791460.02357053-48.99302240.000000e+00
GC_content-0.201658430.02499600 -8.06762937.167628e-16
div_score 0.010388770.02326593 0.44652276.552198e-01
 
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f = fread("/storage11_7T/fuy/TADA-A/cell_WES/cd_mis_pli_syn.7131DNM_6430fam_scaling_factors.txt")
colnames(f)[2] = "z"
f$scaling_factor = f$z * 0.36
fwrite(f[,c(1,3)],"/storage11_7T/fuy/TADA-A/cell_WES/cd_mis_pli_syn.7131DNM_6430fam_scaling_factors_x036.txt",sep="\t")
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system.time(compact_data <- TADA_A_read_info_by_chunks(
mut_files = "/storage11_7T/fuy/TADA-A/cell_WES/cd_mis_pli_syn.7131DNM.allele.bed",
    
# c("db/MS_data/DNM/Jiang_cases_DNM_with_allele_info.txt",
# "db/MS_data/DNM/Kong_cases_DNM_with_allele_info.txt",
# "db/MS_data/DNM/Michaelson_cases_DNM_with_allele_info.txt",
# "db/MS_data/DNM/Yuen_NM2015_cases_DNM_with_allele_info.txt",
# "db/MS_data/DNM/Wu_cases_DNM_with_allele_info.txt"),    
    
window_file =  'db/MS_data/windows_partition/cd_windows_with_div_score.bed',
    
mutrate_scaling_files = c("/storage11_7T/fuy/TADA-A/cell_WES/cd_mis_pli_syn.7131DNM_6430fam_scaling_factors_x036.txt"),  
    
# sample_sizes = 4265,
sample_sizes = 6430,    
    
# mutrate_scaling_files = c("db/MS_data/results/Jiang_windows_mutrate_with_div_score_scaling_file_for_test_DNM.txt",
#                          "db/MS_data/results/Kong_windows_mutrate_with_div_score_scaling_file_for_test_DNM.txt",
#                          "db/MS_data/results/Michaelson_windows_mutrate_with_div_score_scaling_file_for_test_DNM.txt",
#                          "db/MS_data/results/Yuen_NM2015_windows_mutrate_with_div_score_scaling_file_for_test_DNM.txt",
#                          "db/MS_data/results/Wu_windows_mutrate_with_div_score_scaling_file_for_test_DNM.txt"),    
    
# sample_sizes = c(32,78,10,162,32),    
    
    
gene_prior_file = "db/MS_data/prior/uniform_gene_prior.txt",
    
nonAS_noncoding_annotations = NA, #c( 
#                                  "/storage11_7T/fuy/TADA-A/annotation/ccr/ccrs.allchrom.gt90.bed"),
                                #"/storage11_7T/fuy/TADA-A/annotation/ccr/chr_ccr_gt95_syn_rm.bed"),

AS_noncoding_annotations = list(
######################### interaction #####################  
# c("/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex.altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex.altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex.altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex.altT.ccr90.bed") , 
    
# c("/storage11_7T/fuy/TADA-A/annotation/MVP/MVP.altA.ccr90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MVP/MVP.altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MVP/MVP.altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MVP/MVP.altT.ccr90.bed") ,
    
# c("/storage11_7T/fuy/TADA-A/annotation/primateAI/primateAI.altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/primateAI/primateAI.altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/primateAI/primateAI.altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/primateAI/primateAI.altT.ccr90.bed")  ,
    
# c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/MPC2.altA.ccr90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MPC_score/MPC2.altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MPC_score/MPC2.altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MPC_score/MPC2.altT.ccr90.bed") ,   
        
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced5.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced5.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced5.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced5.top5%_altT.ccr90.bed") ,
 

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced6.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced6.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced6.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced6.top5%_altT.ccr90.bed") ,

   
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced7.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced7.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced7.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced7.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced8.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced8.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced8.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced8.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced9.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced9.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced9.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced9.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced10.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced10.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced10.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced10.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced11.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced11.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced11.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced11.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced12.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced12.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced12.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced12.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced13.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced13.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced13.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced13.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced14.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced14.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced14.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced14.top5%_altT.ccr90.bed") ,

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced15.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced15.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced15.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced15.top5%_altT.ccr90.bed") ,

    
# c("/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/A.top001.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/C.top001.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/G.top001.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/T.top001.ccr90.bed") ,
   
    
# c("/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.ccr90.altA.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.ccr90.altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.ccr90.altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.ccr90.altT.bed"),
    
# #c("/storage11_7T/fuy/TADA-A/annotation/ribosnitch/ribosnitch.ccr90.altA.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/ribosnitch.ccr90.altC.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/ribosnitch.ccr90.altG.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/ribosnitch.ccr90.altT.bed"),    
# #
# #c("/storage11_7T/fuy/TADA-A/annotation/CLIPdb/CLIPdb.ccr90.altA.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/CLIPdb/CLIPdb.ccr90.altC.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/CLIPdb/CLIPdb.ccr90.altG.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/CLIPdb/CLIPdb.ccr90.altT.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced1.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced1.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced1.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced1.top5%_altT.ccr90.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced2.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced2.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced2.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced2.top5%_altT.ccr90.bed"),    
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced3.top5%_altA.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced3.top5%_altC.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced3.top5%_altG.ccr90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced3.top5%_altT.ccr90.bed"),   
    
# #c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced4.top5%_altA.ccr90.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced4.top5%_altC.ccr90.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced4.top5%_altG.ccr90.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced/spliced4.top5%_altT.ccr90.bed"),    
    
# c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_A.bed.ccr.gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_C.bed.ccr.gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_G.bed.ccr.gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_T.bed.ccr.gt90.bed") ,   
    
# # c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain12_altA.bed",
# #  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain12_altC.bed",
# #  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain12_altG.bed",
# #  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain12_altT.bed")  ,
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altA.bed.ccr_gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altC.bed.ccr_gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altG.bed.ccr_gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altT.bed.ccr_gt90.bed"),
    
#c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_primateAI_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_primateAI_altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_primateAI_altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_primateAI_altT.bed")，
    
#c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain2_altA_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain2_altC_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain2_altG_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain2_altT_ccr_gt90.bed"),
#    
#c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain3_altA_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain3_altC_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain3_altG_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain3_altT_ccr_gt90.bed"),
#    
#c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain4_altA_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain4_altC_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain4_altG_ccr_gt90.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain4_altT_ccr_gt90.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain5_altA_ccr_gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain5_altC_ccr_gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain5_altG_ccr_gt90.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain5_altT_ccr_gt90.bed"),      
    
######################## DeepSEA #######################

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altA.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain/brain1_altT.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain2_altA.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain2_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain2_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain2_altT.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain3_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain3_altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain3_altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain3_altT.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain4_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain4_altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain4_altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain4_altT.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain5_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain5_altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain5_altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/brain5_altT.bed")

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced1.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced1.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced1.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced1.top5%_altT.bed") ,
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced2.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced2.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced2.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced2.top5%_altT.bed") ,
    
# # c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced3.top5%_altA.bed",
# # "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced3.top5%_altC.bed",
# #  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced3.top5%_altG.bed",
# #  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced3.top5%_altT.bed") ,    
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced4.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced4.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced4.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced4.top5%_altT.bed") ,    
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced5.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced5.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced5.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced5.top5%_altT.bed") ,    
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced6.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced6.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced6.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced6.top5%_altT.bed") ，
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced7.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced7.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced7.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced7.top5%_altT.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced8.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced8.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced8.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced8.top5%_altT.bed") ,
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced9.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced9.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced9.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced9.top5%_altT.bed") ,
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced10.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced10.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced10.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced10.top5%_altT.bed") ,
        
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced11.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced11.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced11.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced11.top5%_altT.bed") ,
        
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced12.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced12.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced12.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced12.top5%_altT.bed") ,
        
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced13.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced13.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced13.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced13.top5%_altT.bed") ,
        
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced14.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced14.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced14.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced14.top5%_altT.bed") ,
        
    
# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced15.top5%_altA.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced15.top5%_altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced15.top5%_altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/spliced_rbp/st.true.spliced15.top5%_altT.bed") ,
        
        
####################### RADAR RBP ############################      
# c("/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/A.top005.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/C.top005.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/G.top005.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/T.top005.bed")    
    
####################### WES denovo ptv ############################    
# c("/storage11_7T/fuy/TADA-A/annotation/pLI/denovo_pLI_snv_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/denovo_pLI_snv_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/denovo_pLI_snv_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/denovo_pLI_snv_alt_A.bed"),
    
####################### gnomad lof (PTV SNV: Nonsense, splice acceptor, and splice donor variants) ############################    
# c("/storage11_7T/fuy/TADA-A/annotation/gnomad/gnomad.v2.1.1.all_lofs_snv_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/gnomad/gnomad.v2.1.1.all_lofs_snv_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/gnomad/gnomad.v2.1.1.all_lofs_snv_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/gnomad/gnomad.v2.1.1.all_lofs_snv_alt_T.bed"), 
    
####################### gnomad PTV tiers ############################
# c("/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt09_gnomad.v2.1.1.all_lofs_snv_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt09_gnomad.v2.1.1.all_lofs_snv_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt09_gnomad.v2.1.1.all_lofs_snv_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt09_gnomad.v2.1.1.all_lofs_snv_alt_T.bed")
    
# c("/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_05_995_gnomad.v2.1.1.all_lofs_snv_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_05_995_gnomad.v2.1.1.all_lofs_snv_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_05_995_gnomad.v2.1.1.all_lofs_snv_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_05_995_gnomad.v2.1.1.all_lofs_snv_alt_T.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_lt05_gnomad.v2.1.1.all_lofs_snv_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_lt05_gnomad.v2.1.1.all_lofs_snv_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_lt05_gnomad.v2.1.1.all_lofs_snv_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_lt05_gnomad.v2.1.1.all_lofs_snv_alt_T.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt_995_gnomad.v2.1.1.all_lofs_snv_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt_995_gnomad.v2.1.1.all_lofs_snv_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt_995_gnomad.v2.1.1.all_lofs_snv_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/pLI/pLI_nlt_995_gnomad.v2.1.1.all_lofs_snv_alt_T.bed"),
    
####################### annova missense ############################
#                       c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_missense_alt_A.bed", 
#                           "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_missense_alt_C.bed", 
#                           "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_missense_alt_G.bed",
#                           "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_missense_alt_T.bed"),

####################### annova lof ############################
# c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_A.bed", 
# "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_C.bed", 
# "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_T.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_A.nlt995.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_C.nlt995.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_G.nlt995.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_T.nlt995.bed") ,
    
c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_A.05-995.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_C.05-995.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_G.05-995.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_T.05-995.bed") ,
    
c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_A.ls05.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_C.ls05.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_G.ls05.bed",
 "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_lof_alt_T.ls05.bed") ,
    
####################### annova syn ############################
                              c("/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_cd_syn_alt_A.bed",
                                "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_cd_syn_alt_C.bed",
                                "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_cd_syn_alt_G.bed",
                                "/storage11_7T/fuy/TADA-A/annotation/driverMAPS/all_cd_syn_alt_T.bed"),
    
####################### CADD ############################
# c("/storage11_7T/fuy/TADA-A/annotation/CADD/whole_genome_SNVs_gt15_altA_within_10kb_and_promoter_no_utr.bed",
# "/storage11_7T/fuy/TADA-A/annotation/CADD/whole_genome_SNVs_gt15_altC_within_10kb_and_promoter_no_utr.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/CADD/whole_genome_SNVs_gt15_altG_within_10kb_and_promoter_no_utr.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/CADD/whole_genome_SNVs_gt15_altT_within_10kb_and_promoter_no_utr.bed"),    

####################### RBP ############################
# c("/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.all.bed.merge_overlap_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altA.bed.merge_in_coding_windows.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.all.bed.merge_overlap_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altC.bed.merge_in_coding_windows.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.all.bed.merge_overlap_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altG.bed.merge_in_coding_windows.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/RBP.all.bed.merge_overlap_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altT.bed.merge_in_coding_windows.bed"),

# ###################### MVP ###########################
#  c("/storage11_7T/fuy/TADA-A/annotation/MVP/chr_MVP_all_rare_missense_pathogen_rank_gt_75_alt_A.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MVP/chr_MVP_all_rare_missense_pathogen_rank_gt_75_alt_C.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MVP/chr_MVP_all_rare_missense_pathogen_rank_gt_75_alt_G.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/MVP/chr_MVP_all_rare_missense_pathogen_rank_gt_75_alt_T.bed"),
    
# # ############################ primateAI ################################
# c("/storage11_7T/fuy/TADA-A/annotation/primateAI/chr_primateAI_exome_mutation_pathogen_rank_gt_80_alt_A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/primateAI/chr_primateAI_exome_mutation_pathogen_rank_gt_80_alt_C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/primateAI/chr_primateAI_exome_mutation_pathogen_rank_gt_80_alt_G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/primateAI/chr_primateAI_exome_mutation_pathogen_rank_gt_80_alt_T.bed"),

# # ########################## spidex #############################
# c("/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex_public_noncommercial_v1_0.tab_alt_A_lower10pct.bed",
# "/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex_public_noncommercial_v1_0.tab_alt_C_lower10pct.bed",
# "/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex_public_noncommercial_v1_0.tab_alt_G_lower10pct.bed",
# "/storage11_7T/fuy/TADA-A/db/MS_data/annota/spidex_public_noncommercial_v1_0.tab_alt_T_lower10pct.bed"),

# ############## MPC ##################
c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/fordist_constraint_official_mpc_values_v2_MPC_gt2_altA.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/fordist_constraint_official_mpc_values_v2_MPC_gt2_altC.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/fordist_constraint_official_mpc_values_v2_MPC_gt2_altG.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/fordist_constraint_official_mpc_values_v2_MPC_gt2_altT.bed"),
    
c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC12_alt_A.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC12_alt_C.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC12_alt_G.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC12_alt_T.bed"),
    
c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC01_alt_A.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC01_alt_C.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC01_alt_G.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/chr.MPC01_alt_T.bed")
    
#################### ribosnitch ###########################
# c("/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altA.bed.merge.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altC.bed.merge.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altG.bed.merge.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.1.altT.bed.merge.bed"),
    
# c("/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altA_in_coding_windows.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altC_in_coding_windows.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altG_in_coding_windows.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altT_in_coding_windows.bed"),
    
###################### CLIPdb ############################
#c("/storage11_7T/fuy/TADA-A/annotation/CLIPdb/human_combine.merged_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altA.bed",
#"/storage11_7T/fuy/TADA-A/annotation/CLIPdb/human_combine.merged_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altC.bed",
#"/storage11_7T/fuy/TADA-A/annotation/CLIPdb/human_combine.merged_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altG.bed",
#"/storage11_7T/fuy/TADA-A/annotation/CLIPdb/human_combine.merged_hg19_refGenes_exons.gtf.lg.transc.fa.RNAsnpM3.bed.abspos.p0.05.merged.altT.bed")
    
),                    

report_proportion = 18665/18665,
#chunk_partition_num =1,
chunk = 2,
node_n = 2,
mutrate_ref_files = c("db/MS_data/mutrate/Example_windows_extended_1bp_for_getting_base_level_mutrate.bed.fasta.tri.alt_A.mutrate.bw",
                   "db/MS_data/mutrate/Example_windows_extended_1bp_for_getting_base_level_mutrate.bed.fasta.tri.alt_C.mutrate.bw",
                   "db/MS_data/mutrate/Example_windows_extended_1bp_for_getting_base_level_mutrate.bed.fasta.tri.alt_G.mutrate.bw",
                   "db/MS_data/mutrate/Example_windows_extended_1bp_for_getting_base_level_mutrate.bed.fasta.tri.alt_T.mutrate.bw")
    
# mutrate_ref_files = c("/storage11_7T/data.for.yuwen/new_mutrate/window.hg19.genome.tri2.alt_A.uq.bedGraph.sort.bw" ,
#                       "/storage11_7T/data.for.yuwen/new_mutrate/window.hg19.genome.tri2.alt_C.uq.bedGraph.sort.bw" ,
#                       "/storage11_7T/data.for.yuwen/new_mutrate/window.hg19.genome.tri2.alt_G.uq.bedGraph.sort.bw" ,
#                       "/storage11_7T/data.for.yuwen/new_mutrate/window.hg19.genome.tri2.alt_T.uq.bedGraph.sort.bw" )
                      

))

saveRDS(compact_data,paste0("/storage11_7T/fuy/TADA-A/cell_WES/",Sys.Date(),"_wes_7131_annovar_pli_6430fam_x036_compact.rds"))
 user   system  elapsed 
3.240    1.049 3426.169 
1
compact_data = readRDS("/storage11_7T/fuy/TADA-A/cell_WES/2020-10-31_wes_7131_annovar_pli_6430fam_x036_compact.rds")
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s = 0
for(j in 1:length(compact_data$base_info)){
    
lg = length(compact_data$base_info[[j]])
for(i in 1:lg){
    if(compact_data$base_info[[j]][[i]]$feature_vector[4] == 1){
        s = s + compact_data$base_info[[j]][[i]]$sum_mut_rate
    }
}
    }
s

604.833220375029

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2
3
605 
1680 * .36 
1756 # obs

605

604.8

1756

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7
RR = TADA_A_RR_estimate(data = compact_data$base_info, selected_annotations = c(seq(1,7)), 
#           gene_prior_file = "db/MS_data/prior/Example_gene_prior.txt", 
        gene_prior_file = "db/MS_data/prior/uniform_gene_prior.txt",
                        optimization_iteration = 2000)

saveRDS(RR,paste0("/storage11_7T/fuy/TADA-A/cell_WES/",Sys.Date(),"_wes_7131_all_mis_pli_6430fam_x036_joint_rr.rds"))
RR
[1] "Read in gene prior file. Time consumed: 0.026s."
[1] "Finished optimization. Time consumed: 15189.986.s"


Warning message in sqrt(c(diag(fisher_info))):
“NaNs produced”


[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
$mle
$par
  1. 2.1424451734737
  2. -1.89705089343724
  3. -3.0922865905406
  4. 2.04079226776
  5. -1.53306735683585
  6. 2.27663122791734
  7. 2.21010014863059
$value
-56129.480681459
$counts
function
730
gradient
<NA>
$convergence
0
$message
NULL
$hessian
A matrix: 7 × 7 of type dbl
-42.93596976-0.0537820597 0.0794061634 0.6889604 4.08241067 -11.56590042 -22.3406114
-0.05378206 0.4779667506-0.0001891749 0.1194076-0.01000444 0.04888898 0.1729131
0.07940616-0.0001891749 1.6719968698 -0.4163940 0.02059096 0.21074811 1.2406163
0.68896043 0.1194075594-0.4163939593-251.9040117-1.07811320 -8.03102921 -16.1118987
4.08241067-0.0100044417 0.0205909600 -1.0781132 9.88774809 0.67822475 -1.0389140
-11.56590042 0.0488889782 0.2107481123 -8.0310292 0.67822475-146.64133960 -9.0523936
-22.34061139 0.1729131327 1.2406162568 -16.1118987-1.03891398 -9.05239358-601.1079640
$rr_report
A data.frame: 7 × 3
logRRlower_boundupper_bound
<dbl><dbl><dbl>
2.1424451.8432112.441680
-1.897051 NaN NaN
-3.092287 NaN NaN
2.0407921.9171272.164457
-1.533067 NaN NaN
2.2766312.1128952.440368
2.2101002.1294272.290773
 
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8
l = length(compact_data$base_info)
l

s = 0
for(i in 1:l){
    s = s + compact_data$base_info[[i]]$`1`$sum_mut_rate
}
s

2035

0.673927544911119

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tm = proc.time()
dfn = c()
for(i in 1:7){
    
RR = TADA_A_RR_estimate(data = compact_data$base_info, selected_annotations = c(i), 
#           gene_prior_file = "db/MS_data/prior/Example_gene_prior.txt", 
        gene_prior_file = "db/MS_data/prior/uniform_gene_prior.txt",
                        optimization_iteration = 2000)
    
dfn = rbind(dfn,RR$rr_report)
    }
proc.time() - tm
# saveRDS(RR,paste0("/storage11_7T/fuy/TADA-A/annotation/results/",Sys.Date(),"_wes_deepsea_brain_RR.rds"))

dfn
[1] "Read in gene prior file. Time consumed: 0.003s."
[1] "Finished optimization. Time consumed: 333.734.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
[1] "Read in gene prior file. Time consumed: 0.005s."
[1] "Finished optimization. Time consumed: 279.076.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
[1] "Read in gene prior file. Time consumed: 0.005s."
[1] "Finished optimization. Time consumed: 347.618.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
[1] "Read in gene prior file. Time consumed: 0.004s."
[1] "Finished optimization. Time consumed: 277.741.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
[1] "Read in gene prior file. Time consumed: 0.005s."
[1] "Finished optimization. Time consumed: 393.818.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
[1] "Read in gene prior file. Time consumed: 0.005s."
[1] "Finished optimization. Time consumed: 289.588.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"
[1] "Read in gene prior file. Time consumed: 0.005s."
[1] "Finished optimization. Time consumed: 290.586.s"
[1] "Got confidence intervals of RR estimates."
[1] "Finished RR estimation!"



     user    system   elapsed 
13733.994    14.261  2212.212
A data.frame: 7 × 3
relative_risklower_boundupper_bournd
<dbl><dbl><dbl>
4.0172503.7944454.240054
2.7755032.2661433.284863
2.5487042.2804672.816942
2.6153402.5026732.728007
3.2581333.0729543.443312
2.7690332.6307162.907349
2.4117902.3324882.491092
 
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16
options(scipen=200)
tm = proc.time()
BF = TADA_A_get_BFs(data = compact_data$base_info,
               selected_annotations = seq(1,7),
               rr = RR$rr_report$logRR, 
#                additional_BF_file = c("/storage11_7T/fuy/TADA-A/annotation/cd_BF/Example_gene_coding_BF.txt"), 
               additional_BF_file = c("/storage11_7T/fuy/TADA-A/annotation/cd_BF/uniform_cd_BFs.txt"),
               TADA_p0 = 0.94)

g_BF = BF$gene_BF_table
g_BF = g_BF[order(g_BF$FDR_all),]
g_BF2 = g_BF[g_BF$FDR_all <= 0.1,]
proc.time() - tm
nrow(g_BF2)

g_BF2
[1] "Read in additional BF file /storage11_7T/fuy/TADA-A/annotation/cd_BF/uniform_cd_BFs.txt."
[1] "Flagged genes that don't have any bases with any informative annotation."
[1] "Got genenames without bases that have informative rr features."
[1] "Got logBF_noncoding."
[1] "Added coding and non-coding logBF. Time consumed: 2.427s."
[1] "Finished!"



   user  system elapsed 
 10.832   0.008  10.073

180

A data.table: 180 × 9
genenamelogBF_noncodinglogBF_codinglogBF_allBF_noncodingBF_codingBF_allFDR_codingFDR_all
<chr><dbl><dbl><dbl><dbl><dbl><dbl><dbl><dbl>
DYNC1H111.720837011.720837123110.43881123110.43880.940.0001272408
ANK2 10.750745010.750745 46664.76551 46664.76550.940.0002314281
ARID1B 10.690188010.690188 43922.76001 43922.76000.940.0002731386
FBN1 9.5970380 9.597038 14721.10731 14721.10730.940.0004706290
MUC2 9.3336720 9.333672 11312.59201 11312.59200.940.0006530976
SETD5 8.5784130 8.578413 5315.66131 5315.66130.940.0010340155
NAV2 8.5215900 8.521590 5022.03391 5022.03390.940.0013305682
SASH1 8.5213580 8.521358 5020.86961 5020.86960.940.0015530726
CACNA1E 8.3111350 8.311135 4068.92961 4068.92960.940.0018066810
MYH9 8.2040690 8.204069 3655.79511 3655.79510.940.0020527276
BCL9L 8.1868040 8.186804 3593.21991 3593.21990.940.0022607647
SCN1A 8.1078570 8.107857 3320.45481 3320.45480.940.0024637070
BRD4 8.0516240 8.051624 3138.88991 3138.88990.940.0026562188
KCNMA1 7.9750310 7.975031 2907.44681 2907.44680.940.0028493162
PXDNL 7.9361930 7.936193 2796.69211 2796.69210.940.0030307385
GRN 7.8843290 7.884329 2655.34211 2655.34210.940.0032079079
PTPRM 7.7512110 7.751211 2324.38551 2324.38550.940.0034130314
SNTG1 7.7252310 7.725231 2264.77541 2264.77540.940.0036050859
PRKCA 7.7113890 7.711389 2233.64251 2233.64250.940.0037819289
SRCAP 7.5894540 7.589454 1977.23441 1977.23440.940.0039858942
PKD2L1 7.5871320 7.587132 1972.64761 1972.64760.940.0041712979
GNS 7.4825710 7.482571 1776.80321 1776.80320.940.0043789784
MYO7B 7.1712140 7.171214 1301.42411 1301.42410.940.0047057577
PTGFRN 7.1002400 7.100240 1212.25751 1212.25750.940.0050412953
GRIK5 7.0822160 7.082216 1190.60451 1190.60450.940.0053591508
UNC45B 7.0640080 7.064008 1169.12191 1169.12190.940.0056616132
FOXK2 7.0000980 7.000098 1096.74081 1096.74080.940.0059735375
TECTA 6.9647410 6.964741 1058.64081 1058.64080.940.0062810196
RELN 6.8667970 6.866797 959.86951 959.86950.940.0066182101
PTPRF 6.8578950 6.857895 951.36201 951.36200.940.0069376308
⋮⋮⋮⋮⋮⋮⋮⋮⋮
TRRAP 4.21003204.21003267.35872167.358720.940.07921092
ADCY2 4.20792704.20792767.21706167.217060.940.07993334
CIT 4.20325704.20325766.90390166.903900.940.08065101
NID2 4.19838704.19838766.57885166.578850.940.08136423
AGAP2 4.18269304.18269365.54212165.542120.940.08208394
TRIO 4.16915504.16915564.66080164.660800.940.08280798
NBEAL2 4.16559704.16559764.43114164.431140.940.08352636
ZNF423 4.16080304.16080364.12297164.122970.940.08424044
AP1B1 4.15869804.15869863.98818163.988180.940.08494761
PSPN 4.14823404.14823463.32205163.322050.940.08565632
C1orf53 4.13355304.13355362.39926162.399260.940.08637078
THAP2 4.12945404.12945462.14396162.143960.940.08708049
PTGES 4.10581604.10581660.69223160.692230.940.08780498
TEX33 4.09916004.09916060.28961160.289610.940.08852726
AKIRIN2 4.09821104.09821160.23245160.232450.940.08924173
PTPRN2 4.09402404.09402459.98079159.980790.940.08995172
PRR23C 4.08961404.08961459.71684159.716840.940.09065756
DLX4 4.08085004.08085059.19576159.195760.940.09136360
CA3 4.06042304.06042357.99884157.998840.940.09208141
ELSPBP1 4.05667804.05667857.78203157.782030.940.09279446
GNRHR 4.05201204.05201257.51308157.513080.940.09350376
DCDC2B 4.04068104.04068156.86508156.865080.940.09421593
LIX1 4.03662804.03662856.63503156.635030.940.09492385
TET2 4.02432604.02432655.94258155.942580.940.09563566
CUL7 4.01394904.01394955.36506155.365060.940.09634951
FCAR 4.01174704.01174755.24332155.243320.940.09705739
HIST1H4E4.00973504.00973555.13226155.132260.940.09775924
KRTAP1-14.00772904.00772955.02175155.021750.940.09845514
SLC35C2 4.00717804.00717854.99147154.991470.940.09914380
OAF 4.00427704.00427754.83218154.832180.940.09982759