COHCAP.BSSeq.preprocess: Preprocessing for Targeted BS-Seq data

In COHCAP: CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Description

WARNING: This function was designed to work with genome_methylation_bismark2bedGraph_v3.pl .bed files (from an earlier version of Bismark) (so, it likely doesn't work with other file formats, such as the coverage files - please see COHCAP.BSSeq_V2.methyl.table() documentation)

Creates custom annotation file as well as COHCAP input file (for COHCAP.annotate).

This function is not necessary for Illumina methylation array analysis.

Output files will be created in specified locations

Usage

COHCAP.BSSeq.preprocess(methyl.folder=getwd(),
				cohcap.inputfile = file.path(getwd(),"BS_Seq_combined.txt"),
				gene.table = file.path(getwd(),"GENCODE_Genes.bed"),
				targeted.regions = file.path(getwd(),"UCSC_CpG_Islands.bed"),
				annotation.file = file.path(getwd(),"COHCAP.targeted.BSSeq.anno.txt"),
				shore.length=2000)

Arguments

methyl.folder	Folder containing .bed files created using genome_methylation_bismark2bedGraph_v3.pl (following Bismark alignment)
cohcap.inputfile	Output file containing a tab-delimited table of percentage methylation values. This table will compatible with the custom annotation file created by this function (annotation.file)
gene.table	.bed file containing gene names and coordinates
targeted.regions	.bed file containing regions selected for targeted BS-Seq
annotation.file	Custom annotation file providing gene and targeted region mappings for CpG sites specifically covered in your Bismark alignment
shore.length	Length of shores considered to be part of the CpG island (in bp upstream and downstream of targeted region coordinates)

Value

This function creates two tab-delimited text files.

One is to be used to as a custom annotation file (annotation.file).

The other is used to create an appropriate input file for COHCAP (cohcap.inputfile).

This function will likely take several hours to run. However, it only needs to be run once.

See Also

Useful Example Files: http://sourceforge.net/projects/cohcap/files/COHCAP_BSSEQ_anno.zip/download *Default settings utilize these files (in current working directory) *These files were created using the UCSC Genome Browser (build hg19)

Raw Data for Demo Dataset: http://www.ncbi.nlm.nih.gov/sra/SRX084504 Full, Formatted Demo Dataset (in standalone package): http://sourceforge.net/projects/cohcap/

Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/

UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start

Examples

library("COHCAP")

dir = system.file("extdata", package="COHCAP")
bed.folder = file.path(dir,"BSSeq")
gene.table = file.path(dir,"GENCODE_Genes_truncated.bed")
targeted.regions = file.path(dir,"UCSC_CpG_Islands_truncated.bed")

output.folder = tempdir()#you may want to use getwd() or specify another folder
annotation.file = file.path(output.folder,"COHCAP.targeted.BSSeq.anno.txt")
cohcap.inputfile = file.path(output.folder,"BS_Seq_combined.txt")

COHCAP.BSSeq.preprocess(bed.folder, cohcap.inputfile, gene.table,
				targeted.regions,annotation.file)

COHCAP documentation built on Nov. 8, 2020, 8:07 p.m.