calculateAlternatePromoterScore: Calculate AP score given a readcount matrix and H3k4me3...

In aditiqamra/APcalc: Calculate APscore

Description

Calculate AP score given a readcount matrix and H3k4me3 annotation

Usage

calculateAlternatePromoterScore(promoterReadCounts, promoterAnnotation,
  promoterMethod = c("medianbased", "rankbased"), medianThreshold, ...)

Arguments

promoterReadCounts	A data.frame object. The number of reads per promoter (rows) for each sample (cols). Rownames should be promoter names
promoterAnnotation	A list with elements. Number of elements equal to nrow @param (promoterReadCounts) and order same as @param promoterReadCounts indicating directionality i.e. 'gain' or 'loss' of promoters in @param promoterReadCounts
promoterMethod	Character type. Identifying method of AP score calculation Can be either "medianbased" or "rankbased"
medianThreshold	A numeric value. Specify if @param promoterMethod is equal to "medianbased"

Value

A data.frame object. An AP score (column) calculated for each sample (rows) using method @param promoterMethod

Author(s)

Aditi Qamra

Examples

## Not run: 
alternatePromoterScore <- calculateAlternatePromoterScore(promoterReadCounts,
                                                         promoterAnnotation,
                                                         promoterMethod = "medianbased",
                                                         medianThreshold = 4)

## End(Not run)

aditiqamra/APcalc documentation built on Jan. 23, 2020, 4:39 p.m.