PerformBinTestAIAnalysisForConditionNPoint: PerformBinTestAIAnalysisForConditionNPoint

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

Description

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

Usage

PerformBinTestAIAnalysisForConditionNPoint(
  inDF,
  vectReps,
  pt = 0.5,
  binNObs = 40,
  Q = 0.95,
  fitCovThr = 50,
  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, ...)
vectReps	A vector (>=2) of replicate numbers for which the analysis should be applied
pt	Optional (default=0.5), a value to compare with
binNObs	Optional (default=40), threshold on number of observations per bin
Q	Optional (default=0.95), confidence level, quantile
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
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 ($CC), (2) ComputeCorrConstantsForAllPairsReps() output ($FitDATA), and (3) PerformBinTestAIAnalysisForConditionNPoint_knownCC() output ($Output).

gimelbrantlab/QCumber documentation built on Feb. 26, 2020, 6:17 p.m.