ComputeCorrConstantsForAllPairsReps: ComputeCorrConstantsForAllPairsReps

In gimelbrantlab/Qllelic: Detects differential allelic imbalance from RNA-seq data

ComputeCorrConstantsForAllPairsReps

Description

Computes QCC for all possible pairs of given replicates.

Usage

ComputeCorrConstantsForAllPairsReps(
  inDF,
  vectReps,
  binNObs = 40,
  fitCovThr = 50,
  EPS = 1.05,
  thr = NA,
  thrUP = NA,
  thrType = "each"
)

Arguments

inDF	Allele counts dataframe: with 2n+1 columns, "ID" and 2n columns with ref & alt counts (rep1_ref, rep1_alt, rep2_ref, rep2_alt, ...)
vectReps	A vector of >= 2 replicate numbers for which the analysis should be applied
binNObs	Optional (default=40), threshold on number of observations per bin
fitCovThr	Optional (default=50), threshold on coverage for genes that will be included in Beta-Bin fitting
EPS	Optional (default=1.05), base of exponent for the coverage binning, setting greater base (1.1 or 1.2 or 1.3) would result in fewer number of coverage bins in fitting process, thus will increase the computational speed, but may potentially reduce accuracy
thr	Optional (default=NA), threshold on the overall number of counts for a gene to be considered in the analysis
thrUP	Optional (default=NA), threshold for max gene coverage (default = NA)
thrType	Optional (default = "each", also can be "average" for average coverage on replicates), threshold type

Value

List of fitting outputs of ComputeCorrConstantFor2Reps() for each combinatorial pair of replicates (in order 1-2,1-3,..,1-N,2-3,..2-N,..,(N-1)-N): list with (1) fitted QCC ($fittedCC) and (2) a table with proportions of observed to expected quantiles per coverage bin ($QObsExpPropsTable).

gimelbrantlab/Qllelic documentation built on Dec. 30, 2024, 4:02 p.m.