getMethylOverlap: Get methylation data overlapping with ChIP-SEQ peaks

In RyDe4/ChIPanalyzer: ChIPAnalyzer

Get methylation data overlapping with ChIP-SEQ peaks

Description

Given paths to a BED file with ChIP-SEQ peaks and a BED file with methylation data, return a dataframe containing methylation data for sites within ChIP-SEQ peaks.

Usage

getMethylOverlap(chipPath, methylPath)

Arguments

chipPath	the path to a BED6 or greater file containing processed ChIP-seq peaks. If data is not stranded, a period should be specified in the strand column.
methylPath	the path to a BED9 file with methylation data similar to those available on the UCSC website, where the ninth column specifies the percentage of reads that were methylated: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/

Value

a dataframe where the first column specifies a chromosome, the second column specifies an end position on the genome, the sixth column represents a strand or . if this is not specified, and the last (ninth) column specifies the percentage of reads that were methylated.

References

H. Pagès, M. Lawrence and P. Aboyoun (2020). S4Vectors: Foundation of vector-like and list-like containers in Bioconductor. R package version 0.24.4.

Lawrence M, Huber W, Pag\'es H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118

Examples

path1 <- system.file("extdata", "MAZ_high_score.bed", package = "ChIPAnalyzer")
path2 <- system.file("extdata", "HcfUMethylData.bed", package = "ChIPAnalyzer")
overlap <- getMethylOverlap(path1, path2)

RyDe4/ChIPanalyzer documentation built on Sept. 1, 2023, 9:18 a.m.