RNA.qc {sRAP} | R Documentation |
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.
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()))
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. |
Charles Warden <cwarden45@gmail.com>
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/
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"))