RNA.qc: Gene Expression Quality Control Statistics

In sRAP: Simplified RNA-Seq Analysis Pipeline

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 <[e-mail]>

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"))

Example output

Loading required package: WriteXLS
NULL
[1] "SRR493372" "SRR493373" "SRR493374" "SRR493375" "SRR493376" "SRR493377"
[1] "integer"
[1] "Group: HOXA1KD"  "Group: scramble"
[1] "Color: green"  "Color: orange"
NULL

sRAP documentation built on April 28, 2020, 9:11 p.m.