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xhmmScripts (version 1.0)

XHMM R scripts

Description

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.

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Version

Install

install.packages('xhmmScripts')

Monthly Downloads

4

Version

1.0

License

GPL-2

Maintainer

Menachem Fromer

Last Published

May 22nd, 2014

Functions in xhmmScripts (1.0)

targetsToSizes

Parse a list of genomic intervals into their corresponding span lengths.
loadXHMMdata

Load all data files generated during an XHMM run.
xhmmScripts-package

Examine and plot XHMM whole-exome-sequencing-based CNV calls
calcSegmentIntervals

Determine all of the indices where a transition in value occurs.
plotAllChromosomeValues

Plot to a png file the values for the given intervals.
plot_XHMM_targets

Plot the XHMM CNV spanning the input target indices.
XHMM_plots

Make a series of plots documenting the output of XHMM.
plot_XHMM_genes

Plot the XHMM CNV spanning the input genes.
readPedigreeFile

Read a Plink/Seq pedinfo file.
loadNamedVectorNoHeaderMayNotExist

Load a vector with named rows.
scanVectorMayNotExist

Read in an unnamed vector.
readPhenotypesFile

Read a Plink/Seq phenotype file.
readNamedMatrix

Quickly read a rectangular matrix that has row and column names.
phenotypeDataToBinarySampleProperties

Convert a parsed Plink/Seq phenotype file into a matrix of binary sample properties.
listOfNulls

Create an empty list object of given size.
pedigreeDataToBinarySampleProperties

Convert a parsed Plink/Seq pedinfo file into a matrix of binary sample properties.
plot_XHMM_region

Plot the XHMM CNV spanning the input region.
loadTargetsToGenes

Load the exome-target to gene mappings.
sourceDir

Run source across the entire set of specified files in a given directory.
loadXCNVcalls

Load the XHMM CNV calls.
targetsToChrBp1Bp2

Parse a list of genomic intervals into their component chromosome, start, and stop.