Man pages for xhmmScripts
XHMM R scripts

calcSegmentIntervalsDetermine all of the indices where a transition in value...
listOfNullsCreate an empty list object of given size.
loadNamedVectorNoHeaderMayNotExistLoad a vector with named rows.
loadTargetsToGenesLoad the exome-target to gene mappings.
loadXCNVcallsLoad the XHMM CNV calls.
loadXHMMdataLoad all data files generated during an XHMM run.
pedigreeDataToBinarySamplePropertiesConvert a parsed Plink/Seq pedinfo file into a matrix of...
phenotypeDataToBinarySamplePropertiesConvert a parsed Plink/Seq phenotype file into a matrix of...
plotAllChromosomeValuesPlot to a png file the values for the given intervals.
plot_XHMM_genesPlot the XHMM CNV spanning the input genes.
plot_XHMM_regionPlot the XHMM CNV spanning the input region.
plot_XHMM_targetsPlot the XHMM CNV spanning the input target indices.
readNamedMatrixQuickly read a rectangular matrix that has row and column...
readPedigreeFileRead a Plink/Seq pedinfo file.
readPhenotypesFileRead a Plink/Seq phenotype file.
scanVectorMayNotExistRead in an unnamed vector.
sourceDirRun source across the entire set of specified files in a...
targetsToChrBp1Bp2Parse a list of genomic intervals into their component...
targetsToSizesParse a list of genomic intervals into their corresponding...
XHMM_plotsMake a series of plots documenting the output of XHMM.
xhmmScripts-packageExamine and plot XHMM whole-exome-sequencing-based CNV calls
xhmmScripts documentation built on May 29, 2017, 3:08 p.m.