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Calculate_psi_of_all_junction.R
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Calculate_psi_of_all_junction.R
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## calculate PSI of AS3
require(parallel)
library(dplyr)
library(plyr)
library(pryr)
require(parallel)
library(ggplot2)
library(cowplot)
library(GenomicRanges)
library(reshape2)
library(vioplot)
depar <- par()
## path and name of SJ merged RData
pfsj <- file.path("/mnt/data5/BGI/UCB/tangchao/data/SJ/SJ(all_more_than_10)_merged_touse.RData")
## path of figure/file output
pffo <- file.path("/mnt/data5/BGI/UCB/tangchao/DSU/")
## path of RData output
pfro <- file.path("/mnt/data5/BGI/UCB/tangchao/DSU/RData/")
## path of gtf
pfgtf <- file.path("/mnt/data1/reference/ensembl/human/Homo_sapiens.GRCh38.87.gtf")
#### 1.load data --------------------------------------------------------------------------------------------------------------------------------
load(pfsj)
SJ_tu -> count_use
require(data.table) # v1.6.6
require(gdata)
f_dowle3 = function(DT) {
# either of the following for loops
# by name :
for (j in names(DT))
set(DT,which(is.na(DT[[j]])),j,0)
# or by number (slightly faster than by name) :
for (j in seq_len(ncol(DT)))
set(DT,which(is.na(DT[[j]])),j,0)
}
f_dowle3(count_use)
#### 2. Identify alternative splicing events ----------------------------------------------------------------------------------------------------
junc=count_use
#junc.names=do.call(rbind,(strsplit(sub(x=rownames(junc),
# pattern="^([[:alnum:]]+):([[:digit:]]+)-([[:digit:]]+)$",
# replace="\\1;\\2;\\3"),split=";")))
junc.names=do.call(rbind,strsplit(rownames(junc),split="[:-]"))
#alnum-- Letters and Numbers；digit -- Numbers
colnames(junc.names) <- c("chr","start","end")
rownames(junc.names) <- rownames(junc)
junc.names=data.frame(junc.names,stringsAsFactors=F)
junc.names$start=as.integer(junc.names$start)
junc.names$end=as.integer(junc.names$end)
junc.names=junc.names[order(junc.names$chr,junc.names$start,junc.names$end),]
junc.names$names=rownames(junc.names)
junc.as_same_start=do.call(c,mclapply(unique(junc.names$chr),function(chr) {
junc.chr=junc.names[junc.names$chr==chr,]
same.start=dlply(junc.chr,c("start"),function(x) x)
#same.end=dlply(junc.chr,c("end"),function(x) {if(nrow(x)>1) {return(x)} else {return(NULL)}})
print(chr)
return(same.start)
},mc.cores=10))
junc.as_same_end=do.call(c,mclapply(unique(junc.names$chr),function(chr) {
junc.chr=junc.names[junc.names$chr==chr,]
#same.start=dlply(junc.chr,c("start"),function(x) x)
same.end=dlply(junc.chr,c("end"),function(x) {if(nrow(x)>1) {return(x)} else {return(NULL)}})
print(chr)
return(same.end)
},mc.cores=10))
psi_sj_same_start=mclapply(junc.as_same_start,function(sjs){
sjs.names=sjs$names[order(as.numeric(sjs$end)-as.numeric(sjs$start))]# find the splicing_in isoform to calculate the psi
tab=as.matrix(t(junc[sjs.names,]))
rs<-apply(tab, 1, function(a) sum(a))
tsrs<-tab/rs
return(t(tsrs))
},mc.cores = 6)
psi_sj_same_end=mclapply(junc.as_same_end,function(sjs){
sjs.names=sjs$names[order(as.numeric(sjs$end)-as.numeric(sjs$start))]# find the splicing_in isoform to calculate the psi
tab=as.matrix(t(junc[sjs.names,]))
rs<-apply(tab, 1, function(a) sum(a))
tsrs<-tab/rs
return(t(tsrs))
},mc.cores = 6)
save(psi_sj_same_start,psi_sj_same_end, file = "/mnt/data5/BGI/UCB/tangchao/DSU/RData/psi_list_left_right.RData")
do.call(rbind,psi_sj_same_start) -> psi_sj_same_start_table
do.call(rbind,psi_sj_same_end) -> psi_sj_same_end_table
length(psi_sj_same_start)
# [1] 368535
length(psi_sj_same_end)
# [1] 368750
dim(psi_sj_same_start_table)
# [1] 460327 3574
dim(psi_sj_same_end_table)
# [1] 146930 3574
save(psi_sj_same_start_table,psi_sj_same_end_table, file = "/mnt/data5/BGI/UCB/tangchao/DSU/RData/psi_list_left_right_table.RData")
#### intron-centric PSI calculation ==============================================================================================================
#### alternative splicing distance is 1 0r 2 bp ==============================
require(parallel)
library(dplyr)
library(plyr)
library(pryr)
require(parallel)
library(ggplot2)
library(cowplot)
library(GenomicRanges)
library(reshape2)
library(vioplot)
pfsj <- file.path("/mnt/data5/BGI/UCB/tangchao/data/SJ/SJ_merged_raw_te(no_NA).RData")
load(pfsj)
require(data.table) # v1.6.6
require(gdata)
f_dowle3 = function(DT) {
# either of the following for loops
# by name :
for (j in names(DT))
set(DT,which(DT[[j]] ==1),j,0)
# or by number (slightly faster than by name) :
for (j in seq_len(ncol(DT)))
set(DT,which(DT[[j]] == 1),j,0)
}
f_dowle3(te_table)
#### 2. Identify alternative splicing events ----------------------------------------------------------------------------------------------------
#junc.names=do.call(rbind,(strsplit(sub(x=rownames(junc),
# pattern="^([[:alnum:]]+):([[:digit:]]+)-([[:digit:]]+)$",
# replace="\\1;\\2;\\3"),split=";")))
junc.names=do.call(rbind,strsplit(rownames(te_table),split="[:-]"))
#alnum-- Letters and Numbers；digit -- Numbers
colnames(junc.names) <- c("chr","start","end")
rownames(junc.names) <- rownames(te_table)
junc.names=data.frame(junc.names,stringsAsFactors=F)
junc.names$start=as.integer(junc.names$start)
junc.names$end=as.integer(junc.names$end)
junc.names <- junc.names[junc.names$chr %in% c(1:22,"X","Y"),]
junc.names=junc.names[order(junc.names$chr,junc.names$start,junc.names$end),]
junc.names$names=rownames(junc.names)
junc.as_same_start=do.call(c,mclapply(unique(junc.names$chr),function(chr) {
junc.chr=junc.names[junc.names$chr==chr,]
same.start=dlply(junc.chr,c("start"),function(x) x)
#same.end=dlply(junc.chr,c("end"),function(x) {if(nrow(x)>1) {return(x)} else {return(NULL)}})
print(chr)
return(same.start)
},mc.cores=4))
junc.as_same_end=do.call(c,mclapply(unique(junc.names$chr),function(chr) {
junc.chr=junc.names[junc.names$chr==chr,]
#same.start=dlply(junc.chr,c("start"),function(x) x)
same.end=dlply(junc.chr,c("end"),function(x) {if(nrow(x)>1) {return(x)} else {return(NULL)}})
print(chr)
return(same.end)
},mc.cores=10))
psi_sj_same_start=mclapply(junc.as_same_start,function(sjs){
sjs.names=sjs$names[order(as.numeric(sjs$end)-as.numeric(sjs$start))]# find the splicing_in isoform to calculate the psi
if(nrow(sjs) == 1){
tsrs <- te_table[sjs.names,]
tsrs[tsrs>0] <- 1
}else{
tab=as.matrix(t(te_table[sjs.names,]))
rs<-apply(tab, 1, function(a) sum(a))
tsrs<-t(tab/rs)
}
return(tsrs)
},mc.cores = 10)
save(psi_sj_same_start, file = "/mnt/data5/BGI/UCB/tangchao/DSU/RData/psi_list_same_start_cutoff2.RData")
psi_sj_same_end=mclapply(junc.as_same_end,function(sjs){
sjs.names=sjs$names[order(as.numeric(sjs$end)-as.numeric(sjs$start))]# find the splicing_in isoform to calculate the psi
tab=as.matrix(t(te_table[sjs.names,]))
rs<-apply(tab, 1, function(a) sum(a))
tsrs<-tab/rs
return(t(tsrs))
},mc.cores = 10)
save(psi_sj_same_end, file = "/mnt/data5/BGI/UCB/tangchao/DSU/RData/psi_list_same_end_cutoff2.RData")
do.call(rbind,psi_sj_same_start) -> psi_sj_same_start_table
do.call(rbind,psi_sj_same_end) -> psi_sj_same_end_table
length(psi_sj_same_start)
# [1] 368535
length(psi_sj_same_end)
# [1] 368750
dim(psi_sj_same_start_table)
# [1] 460327 3574
dim(psi_sj_same_end_table)
# [1] 146930 3574
read.table("/mnt/data5/BGI/UCB/ExpMat_NewID/Cell_type.txt", sep = "\t", header = F, row.names = 1) -> celltype
colnames(celltype) <- "Cell type"
#1:198692374-198696711-198696910-198699563
sum(SJ_tu[,row.names(celltype)]["1:198692374-198696711",]>0 & SJ_tu[,row.names(celltype)]["1:198692374-198699563",]>0 & SJ_tu[,row.names(celltype)]["1:198696910-198699563",]>0 )
sum(te_table[,row.names(celltype)]["1:198692374-198696711",]>0 & te_table[,row.names(celltype)]["1:198692374-198699563",]>0 & te_table[,row.names(celltype)]["1:198696910-198699563",]>0 )
sum(SJ_tu[,row.names(celltype)]["1:198692374-198696711",]>0)