ComputeAICIs: ComputeAICIs

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

ComputeAICIs

Description

Calculates Binomial and QCC-corrected binomial CIs for a given vector of AI estimates, and calculates test statistics for comparison with a point or vector of points, for given QCC.

Usage

ComputeAICIs(
  inDF,
  vectReps,
  vectRepsCombsCC,
  pt = 0.5,
  Q = 0.95,
  BF = T,
  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 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 or a vector of values to compare with (if second, should be compatible with the order and size of genes vector in table of allelic counts)
Q	Optional (default=0.95), confidence level, quantile
BF	Optional (default=True), Bonferroni correction for multiple testing, set False ONLY IF Q is alredy corrected
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

A table with IDs, AI estimates, coverage, test p-value, and Confidence Intervals

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