aggrAcc: Aggregate peak counts to gene features

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

Aggregate peak counts to gene features

Description

Use a peak-count matrix (rows=peaks, columns=samples) and as csAnno object from ChIPseeker to aggregate counts from all or specific features for each gene

Usage

aggrAcc(
  counts,
  anno,
  annoCol = "V4",
  feature = "all",
  method = c("mean", "median", "geoMean", "max", "sum"),
  raw = F,
  geneCol = "SYMBOL"
)

Arguments

counts	count matrix where rows=peaks and columns=individual samples
anno	csAnno object (from ChIPseeker annotatePeak()) containing the annotations for only and all of the peaks in 'counts'
annoCol	column name in anno@anno corresponding to the rownames of counts. Defaults to "V4".
feature	Type of feature to aggregate. 'all" will be all features. Other options include "promoter","intron","intergenic", etc. Default is "all".
method	method to use for aggregating counts. One of "mean","median","geoMean", "max", or "sum". Defaults to "mean"
raw	Boolean indicating if exported object should be whole integers (i.e. raw counts). Default=FALSE.

Value

Data.frame with rows=gene symbols, columns= samples, and aggregated gene counts for each gene in each sample.

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