fractionPlotDf: Plot Dataframe

In AllelicImbalance: Investigates Allele Specific Expression

Description

Summarizes information to ease creating plots

Usage

fractionPlotDf(x, snp, strand = "*", top.fraction.criteria = "maxcount", ...)

## S4 method for signature 'ASEset'
fractionPlotDf(x, snp, strand = "*", top.fraction.criteria = "maxcount", ...)

Arguments

x	ASEset
snp	rownames identifier for ASEset or row number
strand	'+', '-' or '*'
top.fraction.criteria	'maxcount', 'ref' or 'phase'
...	arguments to forward to internal functions

Details

Main purpose is to reduce the amount of overall code and ease maintenance.

top.fraction.criteria can take three options, maxcount, ref and phase. The top allele will be every second row in the data frame, with start from row 2. The maxcount argument will put the allele with most reads on top of the bivariate fraction. Similarly the ref argument will put always the reference allele on top. The phase arguments puts the maternal phase always on top. The top.fraction.criteria for the ref or phase arguments requires that both ref and alt is set in mcols(ASEset).

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples

#test on example ASEset
data(ASEset)
a <- ASEset
df <- fractionPlotDf(a, 1, strand="+")

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.