normaliseGeneExpression {psichomics} | R Documentation

## Filter and normalise gene expression

### Description

Filter and normalise gene expression

### Usage

    normaliseGeneExpression(geneExpr, geneFilter = NULL, method = "TMM",
      p = 0.75, log2transform = TRUE, priorCount = 0.25)

### Arguments

`geneExpr` | Matrix or data frame: gene expression
`geneFilter` | Boolean: filtered genes
`method` | normalization method to be used
`p` | percentile (between 0 and 1) of the counts that is aligned when `method="upperquartile"`
`log2transform` | Boolean: perform log2-transformation?
`priorCount` | Average count to add to each observation to avoid zeroes after log-transformation

### Value

Gene expression filtered and normalised

### Examples

    geneExpr <- readFile("ex_gene_expression.RDS")
    normaliseGeneExpression(geneExpr)

[Package psichomics version 1.6.2 Index]