R scripts for plotting and assessing XHMM whole-exome-sequencing-based CNV calls. XHMM (eXome Hidden Markov Model) is a C++ software package (http://atgu.mgh.harvard.edu/xhmm) written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally). This R package enables the user to visualize both the PCA normalization performed by XHMM and the CNVs it has called.
|Date of publication||2014-06-15 07:38:03|
|Maintainer||Menachem Fromer <email@example.com>|
calcSegmentIntervals: Determine all of the indices where a transition in value...
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...
phenotypeDataToBinarySampleProperties: Convert a parsed Plink/Seq phenotype file into a matrix of...
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...
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...
targetsToChrBp1Bp2: Parse a list of genomic intervals into their component...
targetsToSizes: Parse a list of genomic intervals into their corresponding...
XHMM_plots: Make a series of plots documenting the output of XHMM.
xhmmScripts-package: Examine and plot XHMM whole-exome-sequencing-based CNV calls