metagenomeSeq (version 1.14.0)

cumNormStat: Cumulative sum scaling percentile selection

Description

Calculates the percentile for which to sum counts up to and scale by. cumNormStat might be deprecated one day. Deviates from methods in Nature Methods paper by making use row means for generating reference.

Usage

cumNormStat(obj, qFlag = TRUE, pFlag = FALSE, rel = 0.1, ...)

Arguments

obj

A matrix or MRexperiment object.

qFlag

Flag to either calculate the proper percentile using R's step-wise quantile function or approximate function.

pFlag

Plot the relative difference of the median deviance from the reference.

rel

Cutoff for the relative difference from one median difference from the reference to the next

...

Applicable if pFlag == TRUE. Additional plotting parameters.

Value

Percentile for which to scale data

See Also

fitZig cumNorm cumNormStatFast

Examples

data(mouseData)
p = round(cumNormStat(mouseData,pFlag=FALSE),digits=2)