makeCovList: Function to import coverage matrix to R

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

Function to import coverage matrix to R

Description

This function will import the .mat.gz coverage matrix generated by deeptools computeMatrix command, and split it into a list of coverage matrices - one for each bigwig file input into the command.

Usage

makeCovList(
  matfile,
  header = 3,
  bedfile = NULL,
  sampleTable,
  annobed = F,
  species = "human",
  TxDb = NULL,
  db = NULL
)

Arguments

matfile	Character indicating the path to the matrix file (ending in '.mat.gz')
header	Numeric indicating the size of the header in matfile (i.e. number of lines to skip while reading file in). Default=3
bedfile	Character indicating the path to the bed region files used in computeMatrix (can be left 'NULL' to use regions in .mat.gz file). MUST be same order as .mat.gz regions
sampleTable	data.frame with two columns: sampleName and sampleID. sampleName contains the name that will appear for each sample in the figure. SampleID contains a pattern denoting each unique sample (can be the same as sampleName). NOTE: samples must be the same order as that of bigwigs input into computeMatrix.
annobed	Boolean indicating if bed file should be annotated to include transcript IDs (default=FALSE)
species	Character indicating species if annobed=T. Must be "human" or "mouse". Can set to "other" but TxDb object and annoDb must be provided.
TxDb	TxDb object. Used if species="other", otherwise, "TxDb.Hsapiens.UCSC.hg38.knownGene" or "TxDb.Mmusculus.UCSC.mm10.knownGene" are used.
db	Annotation database (as character) to use if species="other", otherwise "org.Hs.eg.db" or "org.Mm.eg.db" are used - must have corresponding bioconductor package installed.

Value

list of length 3: covList containing list of coverage matrices, bed containing regions for each row of the coverage matrices, and cols: a numeric vector of length 4 providing the suggested column parameters for plotMetaGene() and subsetquent functions. Use only when computeMatrix was executed with 'scale-regions' and NOT 'reference-point'

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