2021-04-06-]ASD-pi0-gama-BFGS-MPC-PTV
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 [17]:
9774/3600
2.715
In [2]:
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)
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()
In [50]:
tmm = proc.time()
for(i in seq(0.13,0.2,0.01)){

    a = c(rep(.1,length(selected_annotations)),i)
    
    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
In [51]:
gm.lst
ll.lst
A matrix: 14 × 6 of type dbl
gama1.2414641.9147891.4707961.4385043.0615590.09045340
gama1.2415311.9148041.4707901.4386833.0615270.09044781
gama1.2414631.9148171.4708091.4385083.0615860.09044820
gama1.2414671.9148011.4707901.4385143.0615640.09045304
gama1.2415411.9148461.4705201.4383393.0616190.09044777
gama1.2414981.9148721.4707131.4384903.0615910.09043731
gama1.2386091.9164751.4697671.4394713.0599220.09053881
gama1.2417901.9142961.4697461.4427863.0610790.09047514
gama1.2414601.9147981.4707511.4384573.0615610.09045324
gama1.2390101.9099851.4666761.4522713.0594290.09082373
gama1.2497431.9221971.4676881.4738293.0616660.08967390
gama1.2440731.9170251.4713701.4766103.0643260.08999948
gama1.2418381.9142311.4665101.4842683.0656190.09019894
gama1.2433241.9125721.4698081.4382333.0632000.09043625
  1. -18366.4579534545
  2. -18366.4579536477
  3. -18366.4579533643
  4. -18366.4579534381
  5. -18366.4579544215
  6. -18366.4579539637
  7. -18366.458576798
  8. -18366.4580386069
  9. -18366.4579534436
  10. -18366.4594715837
  11. -18366.4650300506
  12. -18366.4627531057
  13. -18366.4652447568
  14. -18366.4584803872
In [52]:
plot(ll.lst)
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")
In [53]:
which.max(ll.lst)
var(ll.lst)
max(ll.lst)
min(ll.lst)
3
0.00000730210399725621
-18366.4579533643
-18366.4652447568
In [26]:
plot(ll.lst)

不估pi

In [57]:
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=c(2,3,6,7,8)
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 ,control=list("fnscale"=-1, "maxit" = optimization_iteration))$par
 proc.time() - tm

   user  system elapsed 
667.529   0.332 324.877
In [58]:
tm =  proc.time()
bfgs = optim(rep(0.1, length(selected_annotations)), method="BFGS",fr ,control=list("fnscale"=-1, "maxit" = optimization_iteration))$par
 proc.time() - tm

   user  system elapsed 
161.866   0.072  78.424
In [60]:
df
bfgs
  1. 1.46344565699295
  2. 2.17100445775969
  3. 1.86433338840433
  4. 1.44444592922078
  5. 3.32911087047993
  1. 1.46690498994028
  2. 2.18273087829452
  3. 1.80387262286671
  4. 1.66538188008878
  5. 3.30832674725269
In [20]:
RR$rr_report
A data.frame: 5 × 3
logRRlower_boundupper_bound
<dbl><dbl><dbl>
1.4634461.24574941.681142
2.1710041.95424792.387761
1.8643331.31440462.414262
1.4444460.29737592.591516
3.3291113.06792113.590301
In [61]:
gama
  1. 1.24332446350999
  2. 1.91257190150351
  3. 1.46980806864638
  4. 1.43823296325564
  5. 3.06319957242592
  6. 0.0904362521031876
In [15]:
source("/storage11_7T/fuy/TADA-A/tadaA/R/fr.R")
data=readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/2021-04-08_copy_selected_6788SNV_sf_uni_prior_compact.rds")$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 c(2,3,6,7,8)){
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
  1. 1.62160057753149
  2. 2.32140539589934
  3. 2.08159799794485
  4. 2.20970960035793
  5. 3.49379087799581
In [ ]:
library(tadaA)
In [ ]:
RR = TADA_A_RR_estimate(data = data, selected_annotations = c(2,3,6,7,8) ,

        gene_prior_file = gene_prior_file ,
                        optimization_iteration =  optimization_iteration)
RR
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In [3]:
gm.lst = readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/repo/BFGS_gm.lst.rds")
In [10]:
gama = gm.lst[1,]
gama
  1. 1.2414635748318
  2. 1.91478936217252
  3. 1.47079573353391
  4. 1.43850366574147
  5. 3.06155879430218
  6. 0.0904534047284636
In [11]:
sourceCpp(file="/storage11_7T/fuy/TADA-A/cell_WES/DNM/post.cpp")
gene_prior = fread(gene_prior_file)
gene_prior$prior = rep(gama[6],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$logP_Zg0,pr)
    post.dt = data.table(genename =u,prior = post )   
    post.dt
}
In [12]:
g = post_fr(gama[-6])
g$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$FDR<0.1,]
54
In [13]:
gg = fread("/storage11_7T/fuy/TADA-A/cell_WES/DNM/102gene_pval.txt")
g3[g3$genename %in% gg$gene,]
A data.table: 42 × 4
genenamepriorq0FDR
<chr><dbl><dbl><dbl>
SCN2A 1.00000000.0000000000000026645350.000000000000002664535
CHD8 0.99999870.0000013060493869732070.000000653024694818871
SLC6A1 0.99998700.0000129719437693687210.000004759331053002154
SYNGAP1 0.99997910.0000209454043628154450.000008805849380455477
ARID1B 0.99996800.0000320106581209733680.000013446811128559056
FOXP1 0.99984690.0001531014771365413200.000036722588796556099
GRIN2B 0.99971850.0002814852296807446310.000071688680351440179
ANK2 0.99964450.0003554539635424180940.000107159340750312415
CHD2 0.99870330.0012967247305739615370.000239333272952940083
PTEN 0.99646740.0035326360846420490350.000568663554121851011
DEAF1 0.99164050.0083594603514725029920.001276917808426455796
KCNQ3 0.98747250.0125275206176646003440.002214468042529634580
KDM5B 0.97567940.0243205721082841996860.004537799895493133118
NRXN1 0.97520590.0247940789972470598810.005888218502276728640
DNMT3A 0.96765720.0323428076287083365870.008732549436437767043
ADNP 0.96695110.0330488640727788496320.010083455805123382742
ASH1L 0.95997120.0400287697744675652340.011659524961404654775
DYNC1H1 0.94981740.0501825733925623795880.013585677382962541015
SETD5 0.94251100.0574890341673011118220.015676313420311997759
DYRK1A 0.93865680.0613431587267452282930.017752079116058961522
MYT1L 0.93789370.0621062647582487636910.019680521970067213489
GRIA2 0.93653500.0634650063662026697740.021504875486572858079
DPYSL2 0.92113460.0788654379033209007590.023799297983242779370
TRIP12 0.91697080.0830292298254531324630.026077372284866253555
KMT2C 0.91662220.0833777782542546308520.028199609542991749267
MED13L 0.90467090.0953291020423112644980.030597091417967448718
STXBP1 0.89957230.1004277218200904098210.035083782752027573015
SHANK2 0.89768200.1023179555813904517690.037252627036845717412
CREBBP 0.88238850.1176114897183863083900.043945406579425319582
RORB 0.87669350.1233064514008287426710.046212865002893989408
FOXP2 0.87502910.1249709205920053189940.048400588769258200139
TRAF7 0.86316720.1368328132892914217320.052839610834372517656
SUV420H10.85357670.1464233017238953937780.055239192652052584998
EIF3G 0.83846860.1615314387150772468260.057896498803628203278
RFX3 0.82762260.1723773720769991024680.063335124120153962757
PTK7 0.82701820.1729818069027668769880.065885046975563577032
CACNA1E 0.78721900.2127810135426045912150.076662368425251509185
MKX 0.78125050.2187494940703640367020.079622516876191359869
AP2S1 0.76797980.2320201750777018956380.082732673166018108613
PPP1R9B 0.76754070.2324592775771719965760.085727205254241170551
GNAI1 0.75206950.2479304702026595697010.094690446720863297170
GFAP 0.75095030.2490497200092913754330.097548951781760109836
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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 [ ]: