xhmmScripts: XHMM R scripts

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.

AuthorMenachem Fromer
Date of publication2014-06-15 07:38:03
MaintainerMenachem Fromer <fromer@broadinstitute.org>

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calcSegmentIntervals Man page
listOfNulls Man page
loadNamedVectorNoHeaderMayNotExist Man page
loadTargetsToGenes Man page
loadXCNVcalls Man page
loadXHMMdata Man page
pedigreeDataToBinarySampleProperties Man page
phenotypeDataToBinarySampleProperties Man page
plotAllChromosomeValues Man page
plot_XHMM_genes Man page
plot_XHMM_region Man page
plot_XHMM_targets Man page
readNamedMatrix Man page
readPedigreeFile Man page
readPhenotypesFile Man page
scanVectorMayNotExist Man page
sourceDir Man page
targetsToChrBp1Bp2 Man page
targetsToSizes Man page
XHMM_plots Man page
xhmmScripts Man page
xhmmScripts-package Man page

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