aggregateRegionCounts-DsATAC-method: aggregateRegionCounts-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

aggregateRegionCounts-methods

Description

Agregate counts across a set of regions, e.g. for footprinting analysis

Usage

## S4 method for signature 'DsATAC'
aggregateRegionCounts(
  .object,
  regionGr,
  samples = getSamples(.object),
  countAggrFun = "sum",
  norm = "tailMean",
  normTailW = 0.1,
  kmerBiasAdj = TRUE,
  k = 6,
  sampleCovg = NULL,
  sampleKmerFreqM = NULL,
  regionKmerFreqM = NULL,
  silent = FALSE
)

Arguments

.object	DsATAC object
regionGr	GRanges object specifying the regions to aggregate over
samples	sample identifiers
countAggrFun	aggration function to be used for summarizing the insertion counts at each position. Possible values include "sum", "mean", and "median"
norm	method used for normalizing the resulting position-wise counts. Currently only 'tailMean' is supported, which computes normalization factors as the mean signal in the tails of the window
normTailW	fraction of the region window to be used on each side of the window to be used for normalization if norm is one of 'tailMean'
kmerBiasAdj	compute Tn5 bias and use it to adjust the counts as in Corces, et al., Science, (2018)
k	length of the kmer to be used for sequence bias correction. Only relevant if kmerBiasAdj==TRUE.
sampleCovg	to save compute time, a sample coverage track list (as computed by getCoverage(.object)) can be supplied. If not, it will be computed on the fly.
sampleKmerFreqM	to save compute time, a matrix of sample kmer frequency at insertion sites (as computed by getInsertionKmerFreq(.object, ...)) can be supplied. If not, it will be computed on the fly. Only relevant if kmerBiasAdj==TRUE.
regionKmerFreqM	to save compute time, a matrix of region kmer frequencies (kmers X window width). Must have the same number of rows as the specified (or computed) sampleKmerFreqM (kmers) and the same number of columns as the window width (median width of regionGr). Only relevant if kmerBiasAdj==TRUE.
silent	limit log messages

Value

a data.frame containing position-wise counts (raw, normalized and optionally Tn5-bias-corrected) for each sample

Author(s)

Fabian Mueller

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.