getMACSPeaksAnno: Get MACS peaks annotated

In TapscottLab/SeqPipelineTools: Pipeline tools for RNA-seq or ChIP-seq data

Description

This wrapper function takes the peak files generated by MACS2 as a input. Together with TxDb and Organism packages, it calls ChIPseeker::annotatePeak() to get peaks annotated.

Usage

getMACSPeaksAnno(peakFile, genome = "mm",
                 txdb = NULL, annoDb = NULL,
		 rmsk = NULL, skip = 26,
		 annotate.repeat = TRUE)

Arguments

peakFile	A character string indicating the peak file genereated by MACS.
genome	I should get rid of this argument...
txdb	A TxDb object.
annoDb	A character string indicating the genome annotation package, such as org.hg.eg.db.
rmsk	A GRange instance of repeat masker (RMSK).
skip	An integer specifying the head lines in the peak files subject to be skipped. Default to 26. Make sure to open the .xls peak file to confirm. If the skip lines is wrong, them the function would reture errors.
annotate.repeat	A logical indicating whether to include repeats annoation.

A GRanges instance with annotation.

Chao-Jen Wong

## Not run: library(TxDb.Hsapiens.UCSC.hg19.knownGene) mainDir <- "/fh/fast/tapscott_s/CompBio/ATAC-Seq/hg19.MB135.duxiB" macsDir <- file.path(mainDir,"macs2") peak_file <- list.files(macsDir, pattern=".xls$", full.names=TRUE)[1] df <- getMACSPeaksAnno(peak_file genome="hg", skip=21, txdb=TxDb.Hsapiens.UCSC.hg19.knownGene, annoDb="org.Hs.eg.db", annotate.repeat=FALSE) df ## End(Not run)

~kwd1 ~kwd2

TapscottLab/SeqPipelineTools documentation built on May 16, 2019, 2:28 a.m.