MeanCoverage: MeanCoverage

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

Description

Calculates mean allelic coverage (mat+pat) among given replicates.

Usage

MeanCoverage(df, reps = NA, 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
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 mean allelic coverage for given set of replicates

Examples

MeanCoverage(allelicCountsTable, reps=c(3,4), thr=8)

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