2021-04-06-ccr-spliceai-mpc-ptv-ASD-BFGS
In [1]:
library(Rcpp)
sourceCpp(file="/storage11_7T/fuy/TADA-A/cell_WES/DNM/ll_sum.cpp")
sourceCpp(file="/storage11_7T/fuy/TADA-A/cell_WES/DNM/multi_annota.cpp")
sourceCpp(file="/storage11_7T/fuy/TADA-A/cell_WES/DNM/post.cpp")
In [ ]:
# library(tadaA)
# setwd("/storage11_7T/fuy/TADA-A/annotation")

# system.time(compact_data <- TADA_A_read_info_by_chunks(
# mut_files = "/storage11_7T/fuy/TADA-A/cell_WES/DNM/affected/6788snv.affected.cd.auto.no_pli_rm.allele.bed",
    
# window_file = "/storage11_7T/fuy/TADA-A/db/MS_data/windows_partition/17478gene_hg19.87.auto.exon.wd.bed" ,
    
# mutrate_scaling_files = c("/storage11_7T/fuy/TADA-A/cell_WES/sf_1792_d_2058.1_cd_uniform_scaling_factors.txt"),
 
# sample_sizes = 6430, 
    
# gene_prior_file = "/storage11_7T/fuy/TADA-A/db/MS_data/prior/new_uniform_gene_prior.txt",
      
# nonAS_noncoding_annotations = c("/storage11_7T/fuy/TADA-A/annotation/ccr/ccrs.allchrom.gt90.bed") , 

# AS_noncoding_annotations = lst,                    

# report_proportion = 1, #1000/17484,
# chunk = 20,
# node_n = 2,

# mutrate_ref_files = c("/storage11_7T/fuy/TADA-A/db/MS_data/mutrate/merge/supple3/plus_supple3_uq.17478gene.st.mg.A.bw",
#                      "/storage11_7T/fuy/TADA-A/db/MS_data/mutrate/merge/supple3/plus_supple3_uq.17478gene.st.mg.C.bw",
#                      "/storage11_7T/fuy/TADA-A/db/MS_data/mutrate/merge/supple3/plus_supple3_uq.17478gene.st.mg.G.bw",
#                      "/storage11_7T/fuy/TADA-A/db/MS_data/mutrate/merge/supple3/plus_supple3_uq.17478gene.st.mg.T.bw")

# ))

# saveRDS(compact_data,paste0("/storage11_7T/fuy/TADA-A/cell_WES/DNM/",Sys.Date(),"_copy_selected_6788SNV_sf_uni_prior_compact.rds"))
In [25]:
data=readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/2021-04-08_copy_selected_6788SNV_sf_uni_prior_compact.rds")$base_info
library(data.table)
# selected_annotations=c(2,3,6,7,8)
selected_annotations=seq(2,8)

gene_prior_file = "/storage11_7T/fuy/TADA-A/db/MS_data/prior/new_uniform_gene_prior.txt"
optimization_iteration = 2000

gene_prior = fread(gene_prior_file)
gene_prior = gene_prior[order(gene_prior$genename),]

logP_Zg0 = sumall0(data)

fr_pi <- function(par){

    all_rr = par[1:length(selected_annotations)] 
    gene_prior$prior <- rep(par[length(par)],nrow(gene_prior))
    
    logP_Zg1 = sumall1(data,selected_annotations,all_rr)

    logP_table<-data.table(logP_Zg1 = logP_Zg1, logP_Zg0 = logP_Zg0, genename = names(data))
    logP_table <- logP_table[gene_prior, on = "genename"]
    logP_table <- logP_table[complete.cases(logP_table)]
    idx = match(unique(logP_table$genename),logP_table$genename)
    idx2 = c(idx,nrow(logP_table) + 1)
    pr = logP_table[idx,]$prior
    ll_sum1 <- ll_sum(idx2,logP_table$logP_Zg1,logP_table$logP_Zg0,pr)
    ll_sum1 
    }

gm.lst = c()
ll.lst = c()

tmm = proc.time()
# for(i in seq(0.13,0.2,0.01)){

    a = c(rep(.1,length(selected_annotations)),0.1)
    
    gama = optim(a, fr_pi ,method="BFGS",control=list("fnscale"=-1, "maxit" = optimization_iteration))$par
    gm.lst = rbind(gm.lst,gama)
    ll = fr_pi(gama)
    ll.lst = c(ll.lst,ll)    
#     }
proc.time() - tmm
gm.lst
ll.lst

   user  system elapsed 
440.753   0.160 212.762
A matrix: 1 × 8 of type dbl
gama1.2268981.9082040.7969751.057341.449061.4313923.0343150.09017776
-18363.3781901505
In [26]:
pre = readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/results/1-8_joint_BFGS_pi0_gm.rds")
pre
A matrix: 1 × 9 of type dbl
gama0.37315641.1212241.7462320.75090321.0592991.4088171.3695612.9243240.09438637
In [24]:
saveRDS(gm.lst,"/storage11_7T/fuy/TADA-A/cell_WES/DNM/results/1-8_joint_BFGS_pi0_gm.rds")
In [54]:
# saveRDS(gm.lst,"/storage11_7T/fuy/TADA-A/cell_WES/DNM/repo/BFGS_gm.lst.rds")

# saveRDS(ll.lst,"/storage11_7T/fuy/TADA-A/cell_WES/DNM/repo/BFGS_001-006-0005_ll.lst.rds")

不估pi

In [ ]:
source("/storage11_7T/fuy/TADA-A/tadaA/R/fr.R")
data=readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/2021-04-08_copy_selected_6788SNV_sf_uni_prior_compact.rds")$base_info
library(data.table)
selected_annotations=seq(1,8)
gene_prior_file = "/storage11_7T/fuy/TADA-A/db/MS_data/prior/new_uniform_gene_prior.txt"
optimization_iteration = 2000

gene_prior = fread(gene_prior_file)
gene_prior = gene_prior[order(gene_prior$genename),]

logP_Zg0 = sumall0(data)
tm =  proc.time()
df = optim(rep(0.1, length(selected_annotations)), fr ,method = "BFGS", control=list("fnscale"=-1, "maxit" = optimization_iteration))$par
 proc.time() - tm
In [15]:
df

   user  system elapsed 
325.639   0.108 156.387
  1. 0.400415297020835
  2. 1.34768512689438
  3. 2.01885411446615
  4. 0.933417797621115
  5. 1.14994397415669
  6. 1.7679443260289
  7. 1.68309461873796
  8. 3.18074057681043
In [17]:
sourceCpp(file="/storage11_7T/fuy/TADA-A/cell_WES/DNM/post.cpp")
gene_prior = fread(gene_prior_file)
gene_prior$prior = rep(.06,nrow(gene_prior))

post_fr <- function(x){
    all_rr = x
    logP_Zg1 = sumall1(data,selected_annotations,all_rr)   
    logP_table<-data.table(logP_Zg1 = logP_Zg1, logP_Zg0 = logP_Zg0, genename = names(data))
    logP_table <- logP_table[gene_prior, on = "genename"]
    logP_table <- logP_table[complete.cases(logP_table)]
    u = unique(logP_table$genename)
    idx = match(u,logP_table$genename)
    idx2 = c(idx,nrow(logP_table) + 1)
    pr = logP_table[idx,]$prior 
    post = post(idx2,logP_table$logP_Zg1,logP_table$logP_Zg0,pr)
    post.dt = data.table(genename =u,prior = post )   
    post.dt
}

g = post_fr(df)
g$q0 = 1- g$prior

g2 = g[order(g$q0),]

FDR = c()
for (i in 1:nrow(g2)) FDR[i] <- sum(g2$q0[1:i]) / i
g2$FDR = FDR

nrow(g2[g2$FDR<0.1,])

options(scipen=200)

g3 = g2[g2$FDR<0.1,]
49
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In [ ]:
source("/storage11_7T/fuy/TADA-A/tadaA/R/fr.R")
data=readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/2021-04-08_copy_selected_6788SNV_sf_uni_prior_compact.rds")$base_info
library(data.table)
gene_prior_file = "/storage11_7T/fuy/TADA-A/db/MS_data/prior/new_uniform_gene_prior.txt"
optimization_iteration = 2000

gene_prior = fread(gene_prior_file)
gene_prior = gene_prior[order(gene_prior$genename),]

logP_Zg0 = sumall0(data)


rr.lst = c()
for(selected_annotations in seq(1,8)){
tm =  proc.time()
df = optim(rep(0.1, 1), fr, method = "Brent", lower = -1, upper = 10,
                 control=list("fnscale"=-1, "maxit" = optimization_iteration), hessian = TRUE)$par
rr.lst = c(rr.lst,df)
 proc.time() - tm
    }
rr.lst
In [22]:
rr.lst
  1. 1.89744442472648
  2. 1.62160057753149
  3. 2.32140539589934
  4. 1.99728185580991
  5. 2.80030768299368
  6. 2.08159799794485
  7. 2.20970960035793
  8. 3.49379087799581
In [21]:
gama
  1. 0.373156392496565
  2. 1.12122378096892
  3. 1.74623173563047
  4. 0.750903246827905
  5. 1.05929859390918
  6. 1.40881667747513
  7. 1.36956071013636
  8. 2.92432430377406
  9. 0.0943863699203607

constrain?

In [32]:
selected_annotations=seq(1,8)
In [33]:
sourceCpp(file="/storage11_7T/fuy/TADA-A/cell_WES/DNM/post.cpp")
gene_prior = fread(gene_prior_file)
gene_prior$prior = rep(gama[length(selected_annotations)+1],nrow(gene_prior))

post_fr <- function(x){
    all_rr = x
    logP_Zg1 = sumall1(data,selected_annotations,all_rr)   
    logP_table<-data.table(logP_Zg1 = logP_Zg1, logP_Zg0 = logP_Zg0, genename = names(data))
    logP_table <- logP_table[gene_prior, on = "genename"]
    logP_table <- logP_table[complete.cases(logP_table)]
    u = unique(logP_table$genename)
    idx = match(u,logP_table$genename)
    idx2 = c(idx,nrow(logP_table) + 1)
    pr = logP_table[idx,]$prior 
    post = post(idx2,logP_table$logP_Zg1,logP_table$logP_Zg0,pr)
    post.dt = data.table(genename =u,prior = post )   
    post.dt
}
In [34]:
g = post_fr(gama[-(length(selected_annotations)+1)])
g$q0 = 1- g$prior

g2 = g[order(g$q0),]

FDR = c()
for (i in 1:nrow(g2)) FDR[i] <- sum(g2$q0[1:i]) / i
g2$FDR = FDR

nrow(g2[g2$FDR<0.1,])

options(scipen=200)

g3 = g2[g2$FDR<0.1,]
57
In [10]:
gg = fread("/storage11_7T/fuy/TADA-A/cell_WES/DNM/102gene_pval.txt")
g3[g3$genename %in% gg$gene,]
A data.table: 44 × 4
genenamepriorq0FDR
<chr><dbl><dbl><dbl>
SCN2A 1.00000000.00000000000000044408920.0000000000000004440892
CHD8 0.99999980.00000016291348858832320.0000000814567445162062
SLC6A1 0.99999630.00000367399447587235530.0000012789693216349225
ARID1B 0.99998050.00001953268595766832760.0000058423984806432738
SYNGAP1 0.99996470.00003533525027465955760.0000117409688394465313
GRIN2B 0.99985370.00014625231193843291070.0000341595260226109295
FOXP1 0.99984820.00015182150756376522340.0000509683805284901105
ANK2 0.99935630.00064368870929254473620.0001250584216239969404
CHD2 0.99896950.00103047866815497712880.0002256606712385502886
PTEN 0.99769640.00230362155003327462310.0004334567591180227058
DEAF1 0.98500260.01499737998486672108100.0017574497796406316884
KDM5B 0.98179470.01820525260956196156310.0042430146768090556617
KCNQ3 0.97720990.02279011349843518274840.0055678074497823503916
NRXN1 0.97633230.02366771055909222543080.0067744676570696748738
ASH1L 0.96437790.03562214070961577938590.0099563180204064842538
SETD5 0.96404810.03595187189907789182540.0114005154581104505701
ADNP 0.95844230.04155767262861598254630.0129877342565581106043
TRIP12 0.95317640.04682364200467059589530.0146795296439637349556
MYT1L 0.95163060.04836938678327118434910.0162838085553593282795
DNMT3A 0.94731980.05268024853814901042880.0179381921909406751026
KMT2C 0.94680760.05319243816850838246780.0194709854943131872862
DYNC1H1 0.94475450.05524551375241693040860.0209615908384008405030
DYRK1A 0.92220190.07779805256035388083550.0245790481504272739777
KCNMA1 0.91765840.08234159905165538972940.0267184018875097975543
MED13L 0.91491630.08508374551746356040380.0307220555165332968872
GRIA2 0.89939320.10060679684094298025340.0350845716838346852184
SUV420H10.89477520.10522480905858944133510.0372764541017957806712
SHANK2 0.89009770.10990228167088178512500.0394772367554044462112
STXBP1 0.88879940.11120063445874339702610.0415867484525614741764
CREBBP 0.88678290.11321707069255126931750.0436333290879897459091
FOXP2 0.88324660.11675339326360723024580.0456644419817569049980
RORB 0.88168470.11831534833780932292060.0476279799913799442579
DPYSL2 0.88000730.11999268777173555111660.0495323144066524556628
TRAF7 0.85963980.14036019428202062275800.0518612344034567671058
MKX 0.84881490.15118505977669682849300.0543443300377877691609
PTK7 0.84118730.15881274284066060342720.0568923401061505254472
EIF3G 0.83945090.16054905304725164416620.0593603570809386402174
RFX3 0.83399390.16600605306842663999590.0641076057516582059614
PPP1R9B 0.82431240.17568758557444008605590.0689529286467275015493
CACNA1E 0.78398930.21601072154511280487550.0797907213458106667758
ELAVL3 0.78059010.21940993379917317351870.0825283529625432804577
CTNNB1 0.77979450.22020547702032200465540.0877140961885509301554
AP2S1 0.77482280.22517722235343962111640.0902597096360488598821
NCOA1 0.76976670.23023333597269557415640.0928046846603515357410
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In [12]:
lst = list(
    
# c("/storage11_7T/fuy/TADA-A/annotation/ccr/wd/per_base_uq.wd.ccr.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ccr/wd/per_base_uq.wd.ccr.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ccr/wd/per_base_uq.wd.ccr.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ccr/wd/per_base_uq.wd.ccr.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/CLIPdb/wd/uq.wd.CLIPdb.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/CLIPdb/wd/uq.wd.CLIPdb.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/CLIPdb/wd/uq.wd.CLIPdb.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/CLIPdb/wd/uq.wd.CLIPdb.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HDIV.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HDIV.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HDIV.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HDIV.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HVAR.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HVAR.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HVAR.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/dbNSFP/wd/uq.wd.PPH2_D.HVAR.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.10.altA.bed", ###2
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.10.altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.10.altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.10.altT.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.11.altA.bed",###3
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.11.altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.11.altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.11.altT.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.12.altA.bed", ###4
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.12.altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.12.altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.12.altT.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.8.altA.bed", ###5
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.8.altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.8.altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.8.altT.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.9.altA.bed",###6
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.9.altC.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.9.altG.bed",
# "/storage11_7T/fuy/TADA-A/annotation/DeepSEA/alt/wd/uq.wd.9.altT.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc01.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc01.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc01.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc01.T.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc12.A.bed", ###7
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc12.C.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc12.G.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc12.T.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc2.A.bed", ###8
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc2.C.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc2.G.bed",
"/storage11_7T/fuy/TADA-A/annotation/MPC_score/v1/wd/uq.wd.mpc2.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/MVP/wd/uq.wd.MVP.A.bed", ###9
# "/storage11_7T/fuy/TADA-A/annotation/MVP/wd/uq.wd.MVP.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MVP/wd/uq.wd.MVP.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/MVP/wd/uq.wd.MVP.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HDIV.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HDIV.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HDIV.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HDIV.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HVAR.A.bed", ###10
# "/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HVAR.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HVAR.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/PPH2-PPI/wd/uq.wd.PPI.PPH2_D.HVAR.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/PPI/wd/per_base_uq.wd.PPI.A.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/wd/per_base_uq.wd.PPI.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/wd/per_base_uq.wd.PPI.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/PPI/wd/per_base_uq.wd.PPI.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/primateAI/wd/uq.wd.primateAI.A.bed",  ##### 与MVP大部分重合，MVP rr高
# "/storage11_7T/fuy/TADA-A/annotation/primateAI/wd/uq.wd.primateAI.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/primateAI/wd/uq.wd.primateAI.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/primateAI/wd/uq.wd.primateAI.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/wd/uq.wd.RADAR_RBP.A.bed", ###11
# "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/wd/uq.wd.RADAR_RBP.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/wd/uq.wd.RADAR_RBP.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RADAR_RBP/wd/uq.wd.RADAR_RBP.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/wd/uq.wd.RBP-VarDB.A.bed", ###12
# "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/wd/uq.wd.RBP-VarDB.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/wd/uq.wd.RBP-VarDB.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/RBP-VarDB/wd/uq.wd.RBP-VarDB.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/ribosnitch/wd/uq.wd.ribosnitch.A.bed", ###13
# "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/wd/uq.wd.ribosnitch.C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/wd/uq.wd.ribosnitch.G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/ribosnitch/wd/uq.wd.ribosnitch.T.bed"),

# c("/storage11_7T/fuy/TADA-A/annotation/spidex/wd/uq.wd.spidex_alt_A.bed",  ##### 与ptv大部分重合
# "/storage11_7T/fuy/TADA-A/annotation/spidex/wd/uq.wd.spidex_alt_C.bed",
# "/storage11_7T/fuy/TADA-A/annotation/spidex/wd/uq.wd.spidex_alt_G.bed",
# "/storage11_7T/fuy/TADA-A/annotation/spidex/wd/uq.wd.spidex_alt_T.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_AG.allele.bed.05.altA.bed", ###14
"/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_AG.allele.bed.05.altC.bed",
"/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_AG.allele.bed.05.altG.bed",
"/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_AG.allele.bed.05.altT.bed"),
# 
c("/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_DG.allele.bed.05.altA.bed", ###15
"/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_DG.allele.bed.05.altC.bed",
"/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_DG.allele.bed.05.altG.bed",
"/storage11_7T/fuy/TADA-A/annotation/spliceai/alt/wd/uq.wd.DS_DG.allele.bed.05.altT.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.0-05.A.bed", ###16
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.0-05.C.bed",
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.0-05.G.bed",
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.0-05.T.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.05-995.A.bed", ###17
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.05-995.C.bed",
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.05-995.G.bed",
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.05-995.T.bed"),

c("/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.995.A.bed", ###18
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.995.C.bed",
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.995.G.bed",
"/storage11_7T/fuy/TADA-A/annotation/vep/new_annota/ptv/wd/uq.wd.ptv.995.T.bed")

# c("/storage11_7T/fuy/TADA-A/annotation/PPI/wd/wd.MPC-PPI.altA.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/PPI/wd/wd.MPC-PPI.altC.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/PPI/wd/wd.MPC-PPI.altG.bed",
#  "/storage11_7T/fuy/TADA-A/annotation/PPI/wd/wd.MPC-PPI.altT.bed"),
)
In [ ]:
In [ ]: