COHCAP.qc {COHCAP} | R Documentation |
Provides descriptive statistics (median, top/bottom quartiles, mininum,maximum), sample histograms, sample dendrogram, principal component analysis plot.
Output files will be created in the "QC" subfolder.
COHCAP.qc(sample.file, beta.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. |
beta.table |
Data frame with CpG sites in columns (with DNA methylation represented as beta values or percentage methylation), samples in columns, and CpG site annotations are included (in columns 2-5). The COHCAP.annotate function automatically creates this file. |
project.name |
Name for COHCAP project. This determines the names for output files. |
project.folder |
Folder for COHCAP 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). Remember, COHCAP can only analyze discrete variables categoried with groups (preferably with replicates). |
COHCAP Discussion Group: http://sourceforge.net/p/cohcap/discussion/general/
library("COHCAP") dir = system.file("extdata", package="COHCAP") beta.file = file.path(dir,"GSE42308_truncated.txt") sample.file = file.path(dir,"sample_GSE42308.txt") project.folder = getwd() project.name = "450k_test" beta.table = COHCAP.annotate(beta.file, project.name, project.folder, platform="450k-UCSC") COHCAP.qc(sample.file, beta.table, project.name, project.folder)