NormalizeBeta {MAGeCKFlute}R Documentation

Normalize gene beta scores

Description

Two normalization methods are available. cell_cycle method normalizes gene beta scores based on positive control genes in CRISPR screening. loess method normalizes gene beta scores using loess.

Usage

NormalizeBeta(beta, samples = NULL, method = "cell_cycle",
  posControl = NULL, minus = 0.2)

Arguments

beta

Data frame, in which rows are EntrezID, columns are samples.

samples

Character vector, specifying the samples in beta to be normalized. If NULL (default), normalize beta score of all samples in beta.

method

Character, one of 'cell_cycle'(default) and 'loess'.

posControl

A file path or a character vector, specifying a list of gene entrezids as positive controls used for cell cycle normalization

minus

Numeric, scale for cell cycle normalization. Between 0 and 1.

Details

In CRISPR screens, cells treated with different conditions (e.g., with or without drug) may have different proliferation rates. So we defined a list of core essential genes, which is equally negatively selected between samples with different proliferation rate. Normalization of gene beta scores is performed using these essential genes. cell_cycle in MAGeCKFlute normalizes the beta scores of all genes based on the median beta score of essential genes. After normalization, the beta scores are comparable across samples. loess is another optional normalization method, which is used to normalize array data before.

Value

A data frame with same format as input data beta.

Author(s)

Wubing Zhang

Examples

data(MLE_Data)
# Read beta score from gene summary table in MAGeCK MLE results
dd = ReadBeta(MLE_Data, organism="hsa")
tmp = TransGeneID(rownames(dd), "Symbol", "Entrez")
dd = dd[!(duplicated(tmp)|is.na(tmp)), ]
rownames(dd) = tmp[!(duplicated(tmp)|is.na(tmp))]
samples=c("D7_R1", "D7_R2", "PLX7_R1", "PLX7_R2")
#Cell Cycle normalization
dd_essential = NormalizeBeta(dd, samples=samples, method="cell_cycle")
head(dd_essential)

#Optional loess normalization
dd_loess = NormalizeBeta(dd, samples=samples, method="loess")
head(dd_loess)



[Package MAGeCKFlute version 1.0.1 Index]