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

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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.