-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
cecf991
commit 3e2aa6e
Showing
21 changed files
with
1,091 additions
and
245 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,187 @@ | ||
| library(reshape2) | ||
| calcP <- function(geno_vec, dis_vec, dis_limit=20000){ | ||
|
|
||
| dis_bin <- c(100, 1000, 5000, 10000, 20000, 500000, 1000000000000000000) | ||
| prob_bin <- c(1, 0.93, 0.78, 0.71, 0.69, 0.64, 0) | ||
|
|
||
| prob_bin[dis_bin>dis_limit] <- 0 | ||
|
|
||
| pos_match <- which(geno_vec%in%c("000","111")) | ||
| dis_match <- dis_vec[pos_match] | ||
|
|
||
| match_p <- 0 | ||
| for(pos in dis_match){ | ||
| if(pos<=dis_bin[1]){p <-1} | ||
| else{ | ||
| p <- prob_bin[max(which(pos>=dis_bin))+1] | ||
| } | ||
| match_p <- match_p + p/sqrt(pos) | ||
| } | ||
|
|
||
| pos_mismatch <- which(geno_vec%in%c("010","101")) | ||
| dis_mismatch <- dis_vec[pos_mismatch] | ||
|
|
||
|
|
||
| mismatch_p <- 0 | ||
| for(pos in dis_mismatch){ | ||
| if(pos<=dis_bin[1]){p <-1} | ||
| else{ | ||
| p <- prob_bin[max(which(pos>=dis_bin))+1] | ||
| } | ||
| mismatch_p <-mismatch_p + p/sqrt(pos) | ||
| } | ||
|
|
||
| if(is.na(match_p) | is.na(mismatch_p)){p<-(-1)} | ||
| else{ | ||
| if((match_p + mismatch_p) ==0){ | ||
| p <- (-1) | ||
| }else{ | ||
| p <- match_p/(match_p+mismatch_p) | ||
| } | ||
| } | ||
|
|
||
| return(p) | ||
| } | ||
|
|
||
|
|
||
|
|
||
|
|
||
|
|
||
| args = commandArgs(trailingOnly=TRUE) | ||
|
|
||
| chr <- args[1] | ||
| out <- args[2] | ||
| len <- as.numeric(args[4]) | ||
| bin <- as.numeric(args[5]) | ||
|
|
||
| load(paste0(args[3],chr,".input.image.RDS")) | ||
|
|
||
|
|
||
|
|
||
| germline <- mat_qc[!mat_qc$V4=="0|0" & !mat_qc$V4==".|.",] | ||
|
|
||
| print(dim(germline)) | ||
|
|
||
| y <- germline | ||
| dis <- colsplit(y$V1,":", c("id1","id2"))[,2] | ||
| check <- germline[,c(1,2,3,4)] | ||
| check$prob <- (-1000) | ||
| check$tol <- 0 | ||
| check$dis <- (-1000) | ||
|
|
||
| check$prob_phy <- (-1000) | ||
| check$tol_phy <- 0 | ||
|
|
||
| pos_lst <-list() | ||
| sta <- 0 | ||
| for(i in seq(5,ncol(y),1)){ | ||
| vec <- y[,i] | ||
| pos_lst[[i]] <- which(!vec=="0|0" & !y$V4==".|.") | ||
| sta <- sta + length(which(!vec=="0|0" & !y$V4==".|.")) | ||
| } | ||
|
|
||
|
|
||
| dis_rd <-c() | ||
| trio_hap_rd <-c() | ||
| cnt <- 0 | ||
| dis_limit <- 20000 | ||
|
|
||
| lst <- germline$V2 | ||
| dis_rd2 <-c() | ||
| hap_rd2 <-c() | ||
|
|
||
| for(snv in lst[seq(1,length(lst),bin)]){ | ||
| cnt=cnt+1 | ||
| #print(paste0("scanning ",cnt," now...")) | ||
| snv_index <- which(y$V2==snv) | ||
| snv_index_noMisCol <- which(!y[snv_index,]=="0|0" & !y[snv_index,]=="0/0",) | ||
|
|
||
| # remove the first column since they are not genotypes | ||
| snv_index_noMisCol <- snv_index_noMisCol[snv_index_noMisCol>4] | ||
|
|
||
| geno_vec <-c() | ||
| dis_vec <-c() | ||
| dis_phy1 <- c() | ||
| dis_phy2 <- c() | ||
| # identify haplotypes for each element | ||
| index <-0 | ||
| for(pos in snv_index_noMisCol){ | ||
| # element index (snv_index, pos) | ||
| pos_noMisCol <- pos_lst[[pos]] | ||
| lower_vec <- which(pos_noMisCol<snv_index) | ||
| upper_vec <- which(pos_noMisCol>snv_index) | ||
|
|
||
| if(length(lower_vec)>=1 & length(upper_vec)>=1){ | ||
| lower <- pos_noMisCol[max(lower_vec)] | ||
| upper <- pos_noMisCol[min(upper_vec)] | ||
| tp <- y[snv_index, pos] | ||
| tp <- gsub("/", "|", tp) | ||
| geno <- c(y[lower,pos], tp, y[upper, pos]) | ||
|
|
||
| part <-colsplit(geno,"\\|",c("i1","i2"))[,2] | ||
| part[part>1] <- 1 | ||
| flag <- paste0(part[1],part[2],part[3]) | ||
| hap_rd2 <-c(hap_rd2, abs(part[2]-part[1]), abs(part[3]-part[2])) | ||
| dis_rd2 <-c(dis_rd2, dis[snv_index]-dis[lower], dis[upper]-dis[snv_index]) | ||
|
|
||
| dis_vec <- c(dis_vec, dis[upper]-dis[lower]) | ||
| dis_phy1 <- c(dis_phy1, dis[snv_index]-dis[lower]) | ||
| dis_phy2 <- c(dis_phy2, dis[upper]-dis[snv_index]) | ||
| geno_vec <-c(geno_vec,flag) | ||
| } | ||
| } | ||
|
|
||
| sum <- 0 | ||
| sum_equal <- 0 | ||
|
|
||
| if(!is.null(dis_phy1) & sum(dis_phy1<len)){ | ||
| d_geno <- substr(geno_vec[which(dis_phy1<len)],1,2) | ||
| sum <- length(d_geno) | ||
| sum_equal <- sum(d_geno=="00" | d_geno=="11") | ||
| } | ||
|
|
||
| if(!is.null(dis_phy2) & sum(dis_phy2<len)){ | ||
| d_geno <- substr(geno_vec[which(dis_phy2<len)],2,3) | ||
| sum <- length(d_geno) + sum | ||
| sum_equal <- sum(d_geno=="00" | d_geno=="11") + sum_equal | ||
| } | ||
|
|
||
|
|
||
| if(sum>0){ | ||
| p <- sum_equal/sum | ||
| check$prob_phy[cnt] <- p | ||
| check$tol_phy[cnt] <- sum | ||
| print(paste0("Scan ", cnt,":", snv, " ", sum, " ", p, " ",len)) | ||
| } | ||
|
|
||
| if(length(geno_vec)>0 ){ | ||
| dis_rd <-c(dis_rd, dis_vec) | ||
| trio_hap_rd <-c(trio_hap_rd, geno_vec) | ||
| #print(table(trio_hap_rd)) | ||
| sel <-list() | ||
| sel <- table(geno_vec[dis_vec<1000000]) | ||
|
|
||
| if(length(sel)>0){ | ||
| check$prob[cnt] <- 0 | ||
| check$tol[cnt] <- sum(dis_vec<dis_limit) | ||
| check$dis[cnt] <- median(dis_vec[dis_vec<dis_limit]) | ||
| #print(paste0("Scan ", cnt,":", snv, " ", sum, " ", (p_sum_000 + p_sum_111)/sum)) | ||
|
|
||
| } | ||
| } | ||
| } | ||
|
|
||
|
|
||
|
|
||
| res <-list() | ||
| res$dis <- dis_rd | ||
| res$hap <- trio_hap_rd | ||
| res$check <- check | ||
| res$dis2 <- dis_rd2 | ||
| res$hap2 <- hap_rd2 | ||
| saveRDS(res, file=out) | ||
|
|
||
|
|
||
|
|
||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.