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.
- Menachem Fromer
- Date of publication
- 2014-06-15 07:38:03
- Menachem Fromer <email@example.com>
- Determine all of the indices where a transition in value...
- Create an empty list object of given size.
- Load a vector with named rows.
- Load the exome-target to gene mappings.
- Load the XHMM CNV calls.
- Load all data files generated during an XHMM run.
- Convert a parsed Plink/Seq pedinfo file into a matrix of...
- Convert a parsed Plink/Seq phenotype file into a matrix of...
- Plot to a png file the values for the given intervals.
- Plot the XHMM CNV spanning the input genes.
- Plot the XHMM CNV spanning the input region.
- Plot the XHMM CNV spanning the input target indices.
- Quickly read a rectangular matrix that has row and column...
- Read a Plink/Seq pedinfo file.
- Read a Plink/Seq phenotype file.
- Read in an unnamed vector.
- Run source across the entire set of specified files in a...
- Parse a list of genomic intervals into their component...
- Parse a list of genomic intervals into their corresponding...
- Make a series of plots documenting the output of XHMM.
- Examine and plot XHMM whole-exome-sequencing-based CNV calls
Files in this package