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>
LicenseGPL-2
Version1.1
http://atgu.mgh.harvard.edu/xhmm

View on CRAN

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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