xhmmScripts: XHMM R scripts
Version 1.1

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 07:38:05
MaintainerMenachem Fromer <fromer@broadinstitute.org>
LicenseGPL-2
Version1.1
URL http://atgu.mgh.harvard.edu/xhmm
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("xhmmScripts")

Getting started

Package overview

Popular man pages

loadXCNVcalls: Load the XHMM CNV calls.
phenotypeDataToBinarySampleProperties: Convert a parsed Plink/Seq phenotype file into a matrix of...
plot_XHMM_targets: Plot the XHMM CNV spanning the input target indices.
readPedigreeFile: Read a Plink/Seq pedinfo file.
readPhenotypesFile: Read a Plink/Seq phenotype file.
XHMM_plots: Make a series of plots documenting the output of XHMM.
xhmmScripts-package: Examine and plot XHMM whole-exome-sequencing-based CNV calls
See all...

All man pages Function index File listing

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

Functions

CNVnameToIndex Source code
CNVtoColor Source code
CNVtoWidth Source code
XHMM_plots Man page Source code
calcSegmentIntervals Man page Source code
col2rgbString Source code
listOfNulls Man page Source code
loadNamedVectorNoHeaderMayNotExist Man page Source code
loadTargetsToGenes Man page Source code
loadXCNVcalls Man page Source code
loadXHMMdata Man page Source code
parseRegion Source code
pedigreeDataToBinarySampleProperties Man page Source code
phenotypeDataToBinarySampleProperties Man page Source code
plotAllChromosomeValues Man page Source code
plot_XHMM_genes Man page Source code
plot_XHMM_region Man page Source code
plot_XHMM_targets Man page Source code
plot_XHMM_targets_helper Source code
readNamedMatrix Man page Source code
readPedigreeFile Man page Source code
readPhenotypesFile Man page Source code
regionToFinalInds Source code
regionToStartStopInds Source code
scanVectorMayNotExist Man page Source code
sourceDir Man page Source code
startNewRow Source code
targetsToChrBp1Bp2 Man page Source code
targetsToSizes Man page Source code
xhmmScripts Man page
xhmmScripts-package Man page

Files

NAMESPACE
R
R/loadPseqSampleMetaData.R
R/plotCNV.R
R/sourceDir.R
R/loadNamedVectorNoHeaderMayNotExist.R
R/XHMM_plots.R
R/loadTargetsToGenes.R
R/readNamedMatrix.R
R/scanVectorMayNotExist.R
R/XHMM_functions.R
MD5
DESCRIPTION
man
man/plot_XHMM_genes.Rd
man/readPedigreeFile.Rd
man/readPhenotypesFile.Rd
man/sourceDir.Rd
man/plot_XHMM_targets.Rd
man/phenotypeDataToBinarySampleProperties.Rd
man/XHMM_plots.Rd
man/targetsToSizes.Rd
man/plotAllChromosomeValues.Rd
man/xhmmScripts-package.Rd
man/scanVectorMayNotExist.Rd
man/plot_XHMM_region.Rd
man/loadNamedVectorNoHeaderMayNotExist.Rd
man/loadXCNVcalls.Rd
man/targetsToChrBp1Bp2.Rd
man/pedigreeDataToBinarySampleProperties.Rd
man/loadXHMMdata.Rd
man/calcSegmentIntervals.Rd
man/listOfNulls.Rd
man/loadTargetsToGenes.Rd
man/readNamedMatrix.Rd
xhmmScripts documentation built on May 19, 2017, 12:59 p.m.