Commit b880088c authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Change Annotate Peaks to GTF file reference

parent f6036083
Pipeline #4578 failed with stages
in 697 minutes and 39 seconds
......@@ -10,6 +10,7 @@ All notable changes to this project will be documented in this file.
- Add PlotProfile Option
- Add Python version to MultiQC
- Add and Update tests
- Use GTF files instead of TxDb and org libraries in Annotate Peaks
## [publish_1.0.6 ] - 2019-05-31
### Added
......
......@@ -6,17 +6,11 @@
#* --------------------------------------------------------------------------
#*
#Currently Human or Mouse
# Load libraries
library("ChIPseeker")
# Currently mouse or human
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("TxDb.Mmusculus.UCSC.mm10.knownGene")
library("TxDb.Hsapiens.UCSC.hg38.knownGene")
library("org.Hs.eg.db")
library("org.Mm.eg.db")
library(GenomicFeatures)
# Create parser object
args <- commandArgs(trailingOnly=TRUE)
......@@ -31,14 +25,14 @@ genome_assembly <- args[2]
# Load UCSC Known Genes
if(genome_assembly=='GRCh37') {
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
annodb <- 'org.Hs.eg.db'
txdb <- makeTxDbFromGFF("/project/shared/bicf_workflow_ref/human/GRCh37/gencode.v19.chr_patch_hapl_scaff.annotation.gtf")
sym <- read.table("/project/shared/bicf_workflow_ref/human/GRCh37/genenames.txt", header=T, sep='\t') [,4:5]
} else if(genome_assembly=='GRCm38') {
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
annodb <- 'org.Mm.eg.db'
txdb <- makeTxDbFromGFF("/project/shared/bicf_workflow_ref/mouse/GRCm38/gencode.vM20.annotation.gtf")
sym <- read.table("/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt", header=T, sep='\t') [,4:5]
} else if(genome_assembly=='GRCh38') {
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
annodb <- 'org.Hs.eg.db'
txdb <- makeTxDbFromGFF("/project/shared/bicf_workflow_ref/human/GRCh38/gencode.v25.chr_patch_hapl_scaff.annotation.gtf")
sym <- read.table("/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt", header=T, sep='\t') [,4:5]
}
# Output version of ChIPseeker
......@@ -54,18 +48,18 @@ names(files) <- design$Condition
# Granges of files
peaks <- lapply(files, readPeakFile, as = "GRanges", header = FALSE)
peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb, tssRegion=c(-3000, 3000), verbose=FALSE)
column_names <- c("chr", "start", "end", "width", "strand_1", "name", "score", "strand", "signalValue",
"pValue", "qValue", "peak", "annotation", "geneChr", "geneStart", "geneEnd",
"geneLength" ,"geneStrand", "geneId", "transcriptId", "distanceToTSS",
"ENSEMBL", "symbol", "geneName")
"geneLength" ,"geneStrand", "geneId", "transcriptId", "distanceToTSS", "symbol")
for(index in c(1:length(peakAnnoList))) {
filename <- paste(names(peaks)[index], ".chipseeker_annotation.tsv", sep="")
df <- as.data.frame(peakAnnoList[[index]])
colnames(df) <- column_names
write.table(df[ , !(names(df) %in% c('strand_1'))], filename, sep="\t" ,quote=F, row.names=F)
df_final <- merge(df, sym, by.x="geneId", by.y="ensembl", all.x=T)
colnames(df_final) <- column_names
write.table(df_final[ , !(names(df_final) %in% c('strand_1'))], filename, sep="\t" ,quote=F, row.names=F)
# Draw individual plots
......
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