XHMM R scripts

[Up] [Top]

Documentation for package ‘xhmmScripts’ version 1.1

Help Pages

xhmmScripts-package Examine and plot XHMM whole-exome-sequencing-based CNV calls
calcSegmentIntervals Determine all of the indices where a transition in value occurs.
listOfNulls Create an empty list object of given size.
loadNamedVectorNoHeaderMayNotExist Load a vector with named rows.
loadTargetsToGenes Load the exome-target to gene mappings.
loadXCNVcalls Load the XHMM CNV calls.
loadXHMMdata Load all data files generated during an XHMM run.
pedigreeDataToBinarySampleProperties Convert a parsed Plink/Seq pedinfo file into a matrix of binary sample properties.
phenotypeDataToBinarySampleProperties Convert a parsed Plink/Seq phenotype file into a matrix of binary sample properties.
plotAllChromosomeValues Plot to a png file the values for the given intervals.
plot_XHMM_genes Plot the XHMM CNV spanning the input genes.
plot_XHMM_region Plot the XHMM CNV spanning the input region.
plot_XHMM_targets Plot the XHMM CNV spanning the input target indices.
readNamedMatrix Quickly read a rectangular matrix that has row and column names.
readPedigreeFile Read a Plink/Seq pedinfo file.
readPhenotypesFile Read a Plink/Seq phenotype file.
scanVectorMayNotExist Read in an unnamed vector.
sourceDir Run source across the entire set of specified files in a given directory.
targetsToChrBp1Bp2 Parse a list of genomic intervals into their component chromosome, start, and stop.
targetsToSizes Parse a list of genomic intervals into their corresponding span lengths.
xhmmScripts Examine and plot XHMM whole-exome-sequencing-based CNV calls
XHMM_plots Make a series of plots documenting the output of XHMM.