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.gene_summary)
    # Read beta score from gene summary table in MAGeCK MLE results
    dd = ReadBeta(mle.gene_summary, organism="hsa")
    #Cell Cycle normalization
    dd_essential = NormalizeBeta(dd, samples=c("dmso", "plx"), method="cell_cycle")
    head(dd_essential)

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

[Package MAGeCKFlute version 1.2.3 Index]