normalize_counts: Total count normalization of DNA and RNA counts

In hansenlab/mpra: Analyze massively parallel reporter assays

Total count normalization of DNA and RNA counts

Description

Total count normalization of DNA and RNA counts.

Usage

normalize_counts(object, normalizeSize = 10e6, block = NULL)

Arguments

object	An object of class MPRASet.
normalizeSize	If normalizing, the target library size (default is 10e6).
block	A vector giving the sample designations of the columns of object. The default, NULL, indicates that all columns are separate samples.

Details

block is a vector that is used when the columns of the MPRAset object are paired. This often is the case when comparing allelic versions of an element. In this case, the first $s$ columns of object give the counts for the reference allele in $s$ samples. The second $s$ columns give the counts for the alternative allele measured in the same $s$ samples. With 3 samples, block would be c(1,2,3,1,2,3). All columns are scaled to have 10 million counts.

Value

An object of class MPRASet with the total count-normalized DNA and RNA counts.

Examples

data(mpraSetAggExample)
mpraSetAggExample <- normalize_counts(mpraSetAggExample)

hansenlab/mpra documentation built on Sept. 15, 2024, 4:11 p.m.