PerformBinTestAIAnalysisForTwoConditions_knownCC: PerformBinTestAIAnalysisForTwoConditions_knownCC

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

PerformBinTestAIAnalysisForTwoConditions_knownCC

Description

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

Usage

PerformBinTestAIAnalysisForTwoConditions_knownCC(
  inDF,
  vect1CondReps,
  vect2CondReps,
  vect1CondRepsCombsCC,
  vect2CondRepsCombsCC,
  Q = 0.95,
  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
vect1CondRepsCombsCC	A vector of pairwise-computed correction constants for first condition's tech reps (QCC=1 is no correction)
vect2CondRepsCombsCC	A vector of pairwise-computed correction constants for second condition's tech reps (QCC=1 is no correction)
Q	Optional (default=0.95), confidence level, quantile
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

A table of gene names, AIs + CIs for both conditions, p-values for both non-corrected (BT..) and QCC corrected (BT_CC..) differential tests, classification into genes demonstrating signifficant difference (TRUE) of AI estimates in two conditions, and those that don't (FALSE).

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