addSym: Provide gene symbols for transcripts in metaList

In kevincjnixon/ChIPATAC: Wrapper functions for useful genomic analyses like ChIP-seq or ATAC-seq.

Provide gene symbols for transcripts in metaList

Description

Provide gene symbols for transcripts in metaList

Usage

addSym(
  metaList = NULL,
  bed = NULL,
  covList = NULL,
  cols = NULL,
  species = "hsapiens",
  rmZeroes = T,
  control = "scr_total"
)

Arguments

metaList	object created from makeCovList(). Used by default over 'bed' and 'covList' if provided.
bed	data.frame of regions associated with covList. Leave NULL if providing metaList
covList	list of data.frame coverage matrices. Leave NULL if providing metaList
cols	numeric vector of suggested columns for plotMetaGene() and subsequent functions. leave NULL if providing metaList
species	character indicating species from which to derive gene symbols. At the moment only "hsapiens" or "mmusculus" are accepted.
rmZeroes	Boolean indicating if rows with no coverage are to be removed from coverage matrices. Default=TRUE.
control	character indicating name of control entry from sampleTable given to makeCovList().

Value

Same list object as returned by makeCovList(), but now gene symbols are annotated in $bed object

kevincjnixon/ChIPATAC documentation built on May 25, 2023, 9:33 p.m.