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Analysis function.r
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Analysis function.r
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# Mapping differential methylation sites to gene
###################################################################
# Find each cancer DMP corresponding to the promoter region,
# and write to the file, and then from the genetic level
##################################################################
fileData <- list(
"/home/songy/code_dmr/data_BLCA",
"/home/songy/code_dmr/data_BRCA",
"/home/songy/code_dmr/data_COAD",
"/home/songy/code_dmr/data_ESCA",
"/home/songy/code_dmr/data_HNSC",
"/home/songy/code_dmr/data_KIRC",
"/home/songy/code_dmr/data_KIRP",
"/home/songy/code_dmr/data_LIHC",
"/home/songy/code_dmr/data_LUAD",
"/home/songy/code_dmr/data_LUSC",
"/home/songy/code_dmr/data_PRAD",
"/home/songy/code_dmr/data_THCA",
"/home/songy/code_dmr/data_UCEC")
fileprobe <- "/home/songy/code_dmr/geneTSS/data/probe_full_annotation.txt"
probeData <- read.table(fileprobe, stringsAsFactors = F) # locus info #ID CHR POS QUALITY:GENE:CGI:SPEC:CpGs:DESIGN:TYPE:RANDOM
rownames(probeData) <- probeData[,1]
# gene info
standardGeneData <- read.csv("/home/songy/code_dmr/geneTSS/data/standardGeneData.csv", stringsAsFactors = F)
file_gene <- "/home/songy/code_dmr/geneTSS" # gene info file
sec_file <- "final_DMR_notCpG_mcfs" # CpG island or non CpG island
#sec_file <- "final_DMR_notCpG_mcfs"
#onefile <- "/home/songy/code_dmr/data_COAD"
#x <- FromDMPGetGene(onefile,sec_file,file_gene,probeData,standardGeneData)
allfile <- lapply(fileData, FromDMPGetGene,sec_file,file_gene,probeData,standardGeneData)
################################################################
# The commonalities between cancers were found at the DMP level,
# and then mapped to genes to see the characteristics of pathway
################################################################
fileData <- list(
"/home/songy/code_dmr/data_BLCA",
"/home/songy/code_dmr/data_BRCA",
"/home/songy/code_dmr/data_COAD",
"/home/songy/code_dmr/data_ESCA",
"/home/songy/code_dmr/data_HNSC",
"/home/songy/code_dmr/data_KIRC",
"/home/songy/code_dmr/data_KIRP",
"/home/songy/code_dmr/data_LIHC",
"/home/songy/code_dmr/data_LUAD",
"/home/songy/code_dmr/data_LUSC",
"/home/songy/code_dmr/data_PRAD",
"/home/songy/code_dmr/data_THCA",
"/home/songy/code_dmr/data_UCEC")
fileprobe <- "/home/songy/code_dmr/geneTSS/data/probe_full_annotation.txt"
probeData <- read.table(fileprobe, stringsAsFactors = F) # loci info
rownames(probeData) <- probeData[,1]
standardGeneData <- read.csv("/home/songy/code_dmr/geneTSS/data/standardGeneData.csv", stringsAsFactors = F)
file_gene <- "/home/songy/code_dmr/geneTSS"
sec_file <- "final_DMR_CpG_mcfs"
times <- 10
dmpInf <- GetCombinDMR(times, fileData, sec_file)
fileout_gene <- paste(file_gene, paste0("geneTSS_",dmpInf$tss,"_com_freq_",times,".txt"),sep = "/")
fileout <- DMPtoGene(dmpInf$site_Confirmed, probeData, standardGeneData, fileout_gene)
########################Differentially methylated loci were found in multiple cancers########################
allTimes <- 1:13
sec_file <- "ensemble"
a <- lapply(allTimes, GetCombinDMR,fileData, sec_file,cutoff)
fileData <- list(
"/home/songy/code_dmr/data_BLCA",
"/home/songy/code_dmr/data_BRCA",
"/home/songy/code_dmr/data_COAD",
"/home/songy/code_dmr/data_ESCA",
"/home/songy/code_dmr/data_HNSC",
"/home/songy/code_dmr/data_KIRC",
"/home/songy/code_dmr/data_KIRP",
"/home/songy/code_dmr/data_LIHC",
"/home/songy/code_dmr/data_LUAD",
"/home/songy/code_dmr/data_LUSC",
"/home/songy/code_dmr/data_PRAD",
"/home/songy/code_dmr/data_THCA",
"/home/songy/code_dmr/data_UCEC")
GetSampleNumber <- function(filedata){
load(file.path(filedata,"trainData.Rdata"))
num <- dim(trainData)[2]
cat(filedata, " ",num,"\n" )
return(num)
}
num <- lapply(fileData,GetSampleNumber)
# fileData <- "F:/ChAMP_data_DMRs/1new_code_LR/data/refFlat_hg19.txt"
#
# data <- read.table(fileData)
# data <- data[,1:6]
#
# StandardGeneData <- function(x){
# # str(x)
# # cat(x)
# if(x[4] == "+"){
# a <- as.numeric(x[5])
# geneD = c(a-2500, a+500)
# }
# else{
# a <- as.numeric(x[6])
# geneD = c(a-500, a + 2500)
# }
# # cat("sadf:",geneD, "\n")
# return(c(x[1], x[2], x[3], geneD))
#
# }
# standardGeneData <- apply(data, 1, StandardGeneData)
# standardGeneData <- t(standardGeneData)
# colnames(standardGeneData) <- c("gene_name", "gene_info", "chr", "TSS_start", "TSS_end")
# standardGeneData <- as.data.frame(standardGeneData)
# # standardGeneData$TSS_start <- as.numeric(standardGeneData$TSS_start)
# # standardGeneData$TSS_end <- as.numeric(standardGeneData$TSS_end)
#
# fileW <- "F:/ChAMP_data_DMRs/1new_code_LR/data/standardGeneData.csv"
# write.csv(standardGeneData, file = fileW, row.names = F, quote = F)
SureDMRtoGene <- function(oneDMR, standardGeneData, probeData){
probe <- probeData[oneDMR,]
probe <- as.matrix(probe)
site_num <- as.numeric(probe[1,3])
gene <- subset(standardGeneData, chr == as.character(probe[1,2]) & TSS_start <= site_num & TSS_end >= site_num)
if(dim(gene)[1] < 1){
gene_name <- c("-1")
gene_info <- c("-1")
chr <- c("-1")
TSS_start <- c(-1)
TSS_end <- c(-1)
site <- rep(as.character(probe[1,1]), 1)
site_num <- rep(site_num, 1)
gene <- data.frame(gene_name, gene_info, chr, TSS_start, TSS_end, site, site_num)
}
else{
gene$site <- rep(as.character(probe[1,1]), dim(gene)[1])
gene$site_num <- rep(site_num, dim(gene)[1])
}
return(gene)
}
DMPtoGene <- function(comDMR, probeData, standardGeneData,fileout_gene){
gene_site <- lapply(comDMR, SureDMRtoGene, standardGeneData, probeData)
gene_site <- Reduce(rbind, gene_site)
name <- c("site", "site_num", "gene_name", "gene_info", "chr", "TSS_start", "TSS_end")
gene_site <- gene_site[name]
xx <- gene_site[,3]
k1 <- table(xx)
a <- names(k1)
a <- a[which(a!="-1")]
cat("tss_number:", length(a), " ")
a <- matrix(a, nrow = length(a), ncol = 1)
a <- as.data.frame(a)
#str(a)
xxx <- xx[xx=="-1"]
cat("not_tssNumber:", length(xxx),"\n")
write.table(a, file = fileout_gene, row.names = F, col.names = F, quote = F,sep = "\t")
return(fileout_gene)
}
FromDMPGetGene <- function(onefile,sec_file,file_gene,probeData,standardGeneData){
dmpInf <- GetCanserDMP(onefile,sec_file)
#str(dmpInf)
canser <- strsplit(onefile,split = "_")[[1]]
canser <- canser[length(canser)]
cat(canser," ")
fileout_gene <- paste(file_gene, paste0("geneTSS_",dmpInf$tss,"_",canser,".txt"),sep = "/")
fileout <- DMPtoGene(dmpInf$site_Confirmed, probeData, standardGeneData,fileout_gene)
return(fileout)
}
############## DMP Common ###########################
GetCanserDMP <- function(onefile,sec_file){
namef <- load(paste(onefile, paste0(sec_file,".Rdata"), sep="/"))
if(namef == "final_DMR_CpG_mcfs"){
site_Confirmed <- final_DMR_CpG_mcfs
tss <- "CpG"
}
if(namef == "final_DMR_notCpG_mcfs"){
site_Confirmed <- final_DMR_notCpG_mcfs
tss <- "notCpG"
}
if(namef == "final_DMR_gene_mcfs"){
site_Confirmed <- final_DMR_gene_mcfs
tss <- "gene"
}
if(namef == "final_DMR_notGene_mcfs"){
site_Confirmed <- final_DMR_notGene_mcfs
tss <- "notGene"
}
if(namef == "final_DMR_TSS_mcfs"){
site_Confirmed <- final_DMR_TSS_mcfs
tss <- "TSS"
}
return(list(site_Confirmed=site_Confirmed,tss=tss))
}
GetCombinDMR <- function(times, fileData, whichSec){
all_fea <- lapply(fileData, GetCanserDMP, whichSec)
area <- all_fea[[1]]$tss
all_fea <- unlist(lapply(all_fea, function(x){x$site_Confirmed}))
fea_table <- sort(table(all_fea),decreasing=T)
select_fea <- fea_table[which(fea_table>=times)]
select_fea <- names(select_fea)
cat(area, " ",times, " ", length(select_fea),"\n")
site_Confirmed=select_fea
tss=area
return(list(site_Confirmed=site_Confirmed,tss=tss))
}