XHMM_plots

PLOT_PATH

JOB_PREFICES

JOB_TARGETS_TO_GENES

SAMPLE_FEATURES

SQ_THRESH

NUM_ADD_TARGS

PLOT_READ_DEPTHS

PLOT_PC_CORRS

PLOT_ALL_CNVS

USE_XCNV_TO_PLOT

INCLUDE_PEDIGREE_SAMPLES

PLOT_ONLY_PNG

LIMIT_MEMORY


Make a series of plots documenting the output of XHMM.


 ~kwd1 

 ~kwd2 

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

xhmmScripts

XHMM R scripts

XHMM_plots function

XHMM_plots: Make a series of plots documenting the output of XHMM.

Description

Usage

Arguments

Examples