PerformBinTestAIAnalysisForConditionNPoint_knownCC: PerformBinTestAIAnalysisForConditionNPoint_knownCC

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

PerformBinTestAIAnalysisForConditionNPoint_knownCC

Description

Performs Binomial and QCC-corrected binomial tests (with Bonferroni correction) with a given point estimate, for given QCC.

Usage

PerformBinTestAIAnalysisForConditionNPoint_knownCC(
  inDF,
  vectReps,
  vectRepsCombsCC,
  pt = 0.5,
  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, ...)
vectReps	A vector (>=2) of replicate numbers for which the analysis should be applied
vectRepsCombsCC	A vector of pairwise-computed correction constants for given replicates (QCC=1 is no correction)
pt	Optional (default=0.5), a value to compare with
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, p-values for both non-corrected and (BT..) and QCC corrected (BT_CC..) tests, classification into genes demonstrating signifficant difference (TRUE) from point estimate AI and those that don't (FALSE).

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