ThresholdingCounts: ThresholdingCounts

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

Description

Takes allelic counts table and returns table, where all genes that don't pass a given coverage threshold have NA coverage. Can be restricted to particular replicates.

Usage

ThresholdingCounts(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

Allelic counts table with masked with NA undercovered genes, for selected replicates

Examples

ThresholdingCounts(df = allelicCountsTable, reps = c(1,2), thr = 10)

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