Last data update: 2014.03.03

 R: Prepares output files and plots from MultiPhen results
mPhen.writeOutputR Documentation

Prepares output files and plots from MultiPhen results

Description

Writes output to files defined in mPhen.openOutputConnection, and extracts pvalues and betas for further plots.

Usage

mPhen.writeOutput(results,
output = getOption("mPhen.resultsName","resultsDir/"),geno = NULL,
towrite = list(long.txt = getOption("mPhen.writeLong",TRUE),
qc.txt =  getOption("mPhen.writeQC",FALSE), 
wide.txt = getOption("mPhen.writeWide",TRUE)),
toplot = list(.manh = TRUE, .qq = TRUE,.heatm = TRUE,
              
              .fprint = !is.null(geno)),
opts = mPhen.options("plot"))

Arguments

results

Output of mPhen.assoc

output

Directory to write results, or object returned by mPhen.writeOutput(..)

towrite

List specifying which formats to write output - long.txt and wide.txt for standard results; qc.txt for per-sample qc output.

toplot

List specifying which formats to plot output - .qq for qq plot, .manh for manhattan; .heatm for pvalue heatmap; .fprint for fingerprint plot

geno

Genotype matrix. Note that attr(geno,"closeConnection") controls whether plots are produced, as this indicates whether all batches of genotype data have been analysed

opts

A list of options, which is obtained from mPhen.options("plot"). To get more information about these options, type mPhen.options("plot",descr=TRUE)

Value

Returns an outputConnection, which can be used to write further results.

Results


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO