mPhen.writeOutput {MultiPhen} | R 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.