RNA.qc {sRAP} | R Documentation

## Gene Expression Quality Control Statistics

### Description

Provides descriptive statistics (median, top/bottom quartiles, mininum,maximum), sample histograms and box-plot, sample dendrogram, principal component analysis plot.

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

### Usage

    RNA.qc(sample.file, expression.table, project.name, project.folder, plot.legend = TRUE, color.palette = c("red", "blue", "green", "orange", "purple", "cyan", "pink", "maroon", "yellow", "grey", "black", colors()))

### Arguments

`sample.file` | Tab-delimited text file providing group attributions for all samples considered for analysis.
`expression.table` | Data frame with genes in columns and samples in rows. Data should be log2 transformed. The RNA.norm function automatically creates this file.
`project.name` | Name for sRAP project. This determines the names for output files.
`project.folder` | Folder for sRAP output files
`plot.legend` | A logical value: Should legend be plotted within QC figures?
`color.palette` | Colors for primary variable (specified in the second column of the sample file). If the primary variable is a continuous variable, this parameter is ignored.

### Author(s)

Charles Warden <cwarden45@gmail.com>

### 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")
    library("WriteXLS")

    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)

    RNA.qc(sample.table, expression.mat, project.name, project.folder, plot.legend=FALSE, color.palette=c("green","orange"))

[Package sRAP version 1.24.0 Index]