CountsToAI: CountsToAI

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

Description

Calculates allelic imbalances from merged counts over given replicates (ai(sum_reps(gene))).

Usage

CountsToAI(
  df,
  reps = NA,
  meth = "mergedToProportion",
  thr = NA,
  thrUP = NA,
  thrType = "each"
)

Arguments

df	Allele counts dataframe: with 2n+1 columns, "ID" and 2n columns with ref & alt counts (rep1_ref, rep1_alt, rep2_ref, rep2_alt, ...)
reps	Optional (default=NA, all replicates), a vector of replicate numbers for which the analysis should be applied
meth	Optional (default="mergedToProportion", also can be "meanOfProportions"), method to use, either sum(m)/sum(p) (default), or sum(m/p)
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 and calculated AI estimate for given set of replicates

Examples

CountsToAI(allelicCountsTable, reps=c(1,2), thr=10, thrUP=1000)

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