medianNormalization {CEDA}

Median normalization of sgRNA counts

Description

This function adjusts sgRNA counts by the median ratio method. The normalized sgRNA read counts are calculated as the raw read counts devided by a size factor. The size factor is calcuated as the median of all size factors caculated from negative control sgRNAs (eg., sgRNAs corresponding to non-targeting or non-essential genes).

Usage

medianNormalization(data, control)

Arguments

data

A numeric matrix containing raw read counts of sgRNAs with rows corresponding to sgRNAs and columns correspondings to samples.

control

A numeric matrix containing raw read counts of negative control sgRNAs with rows corresponding to sgRNAs and columns corresponding to samples. Sample ordering is the same as in data.

Value

A list with two elements: 1) size factors of all samples; 2) normalized counts of sgRNAs.

Examples

count <- matrix(rnbinom(5000 * 6, mu=500, size=3), ncol = 6)
colnames(count) = paste0("sample", 1:6)
rownames(count) = paste0("sgRNA", 1:5000)
control <- count[1:100,]
normalizedcount <- medianNormalization(count, control)