xhmmScripts: XHMM R scripts

Share:

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.

Author
Menachem Fromer
Date of publication
2014-06-15 07:38:03
Maintainer
Menachem Fromer <fromer@broadinstitute.org>
License
GPL-2
Version
1.1
URLs

View on CRAN

Man pages

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

Files in this package

xhmmScripts
xhmmScripts/NAMESPACE
xhmmScripts/R
xhmmScripts/R/loadPseqSampleMetaData.R
xhmmScripts/R/plotCNV.R
xhmmScripts/R/sourceDir.R
xhmmScripts/R/loadNamedVectorNoHeaderMayNotExist.R
xhmmScripts/R/XHMM_plots.R
xhmmScripts/R/loadTargetsToGenes.R
xhmmScripts/R/readNamedMatrix.R
xhmmScripts/R/scanVectorMayNotExist.R
xhmmScripts/R/XHMM_functions.R
xhmmScripts/MD5
xhmmScripts/DESCRIPTION
xhmmScripts/man
xhmmScripts/man/plot_XHMM_genes.Rd
xhmmScripts/man/readPedigreeFile.Rd
xhmmScripts/man/readPhenotypesFile.Rd
xhmmScripts/man/sourceDir.Rd
xhmmScripts/man/plot_XHMM_targets.Rd
xhmmScripts/man/phenotypeDataToBinarySampleProperties.Rd
xhmmScripts/man/XHMM_plots.Rd
xhmmScripts/man/targetsToSizes.Rd
xhmmScripts/man/plotAllChromosomeValues.Rd
xhmmScripts/man/xhmmScripts-package.Rd
xhmmScripts/man/scanVectorMayNotExist.Rd
xhmmScripts/man/plot_XHMM_region.Rd
xhmmScripts/man/loadNamedVectorNoHeaderMayNotExist.Rd
xhmmScripts/man/loadXCNVcalls.Rd
xhmmScripts/man/targetsToChrBp1Bp2.Rd
xhmmScripts/man/pedigreeDataToBinarySampleProperties.Rd
xhmmScripts/man/loadXHMMdata.Rd
xhmmScripts/man/calcSegmentIntervals.Rd
xhmmScripts/man/listOfNulls.Rd
xhmmScripts/man/loadTargetsToGenes.Rd
xhmmScripts/man/readNamedMatrix.Rd