PerformBinTestAIAnalysisForTwoConditions: PerformBinTestAIAnalysisForTwoConditions

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

PerformBinTestAIAnalysisForTwoConditions

Description

Calculates QCC. Performs differential tests (with Bonferroni correction) for AI values for two conditions.

Usage

PerformBinTestAIAnalysisForTwoConditions(
  inDF,
  vect1CondReps,
  vect2CondReps,
  binNObs = 40,
  fitCovThr = 50,
  Q = 0.95,
  EPS = 1.05,
  thr = NA,
  thrUP = NA,
  thrType = "each",
  minDifference = NA
)

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, ...)
vect1CondReps	A vector (>=2) of replicate numbers that should be considered as first condition's tech reps
vect2CondReps	A vector (>=2) of replicate numbers that should be considered as second condition's tech reps
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
Q	Optional (default=0.95), confidence level, quantile
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
minDifference	Optional (default=NA), if specified, one additional column is added to the output (T/F depending if the gene changed AI expression more than minDifference in addition to passing the test)

Value

List of (1) fitted QCC for all combanatorial pairs of replicates for both conditions ($CC), (2) ComputeCorrConstantsForAllPairsReps() output for both conditions ($FitDATA), and (3) PerformBinTestAIAnalysisForTwoConditions_knownCC() output ($Output).

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