RNA.norm {sRAP} | R Documentation

## Normalization for RNA-Seq Data

### Description

Takes a table of RPKM (Read Per Kilobase per Million reads [1]) gene expression values. Rounds RPKM values based upon RPKM.cutoff(to avoid bias from low-coverage genes), and then performs a log2 transformation of the data (so that the data more closely follows a normal distribution). The efficacy of this protocol is described in [2].

Output files will be created in the "Raw_Data" subfolder.

### Usage

    RNA.norm(input.file, project.name, project.folder, RPKM.cutoff = 0.1)

### Arguments

`input.file` | Table of RPKM expression values. Genes are represented in columns. Samples are represented in rows.
`project.name` | Name for sRAP project. This determines the names for output files.
`project.folder` | Folder for sRAP output files
`RPKM.cutoff` | Cut-off for rounding RKPM expression values. If the default of 0.1 is used, genes with expression values consistently below 0.1 will essentially be ignored.

### Value

Data frame of normalized expression values on a log2 scale.

Just like the input table, genes are represented on columns, samples are represented in rows.

This data frame is used for quality control and differential expression analysis.

### Author(s)

Charles Warden <cwarden45@gmail.com>

### References

[1] Mortazavi A, Williams BA, McCue K, Schaeffer L, and Wold B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth, 5:621-628.

[2] Warden CD, Yuan Y-C, and Wu X. (2013). Optimal Calculation of RNA-Seq Fold-Change Values. Int J Comput Bioinfo In Silico Model, 2(6): 285-292

### See Also

sRAP goes through an entire analysis for an example dataset provided with the sRAP package.

Please post questions on the sRAP discussion group: http://sourceforge.net/p/bdfunc/discussion/srap/

### Examples

    library("sRAP")

    dir <- system.file("extdata", package="sRAP")
    expression.table <- file.path(dir,"MiSeq_cufflinks_genes_truncate.txt")
    sample.table <- file.path(dir,"MiSeq_Sample_Description.txt")
    project.folder <- getwd()
    project.name <- "MiSeq"

    expression.mat <- RNA.norm(expression.table, project.name, project.folder)

[Package sRAP version 1.20.0 Index]