Gene Expression Quality Control Statistics

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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

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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

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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"))