Man pages for xhmmScripts
XHMM R scripts
| 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 |
