Man pages for Halvee/rvatk
Rare Variant Analysis Toolkit
| AddLooMafCol | add a leave-one-out minor allele freq. column with values to... |
| ApplyThreshold | subset on input table on a user defined condition. |
| BurdenTest | perform a case/control burden test on aggregated rare variant... |
| CollapsingMatrixInit | initializes data frame with discrete genes as rows and... |
| CollapsingMatrixRead | read in a collapsing matrix file from file (gzip detection... |
| CollapsingMatrixRecode | recode a collapsing matrix using a qualvar data frame. |
| CollapsingMatrixShrink | take a subset of collapsing matrix where each gene has at... |
| CollapsingMatrixWrite | write collapsing matrix to output filename (gzipping... |
| GetAlleleCounts | for input variant calls and genotypes, return genotype... |
| PlinkBedAlleleSum | get sum of allele counts across plinkbed for user-defined... |
| PlinkBedCalls | return variant calls per sample that match user-defined... |
| PlinkBedGtsTransform | return genotypes from plinkbed into counts that are expected. |
| PlinkBedInit | functions for working with plinkbed, a snpMatrix object... |
| PlinkBedSubset | subset plinkbed on user-defined set of samples and variants. |
| PlinkBedToQualvar | convert plinkbed data to qualvar data frame and return. |
| ProcessString | convert process input string into a form more agreeable with... |
| QualvarRead | read a file of format qualvar into a qualvar dataframe. |
| QualvarSubset | subset qualvar dataframe on user-defined sets of samples and... |
| QualvarToCollapsingMatrix | convert qualvar dataframe to collapsing matrix data frame. |
| ReadConditionFile | read in a .condition file, where each line represents... |
| ReadGenesetsFile | read genesets file to a list of genesets. |
| ReadLargeTable | read a large table (can be gzipped and/or GB in size) into a... |
| ReadListFile | read in a file where each line is a seperate entry into a... |
| SamplepedIidFidList | table sampleped data frame and get list of individual ID ->... |
| StringToSet | split string to vector |
| TblCndSubset | subset on table based on rows in condition data frame. |
| UpdateTable | update input table with values of res.list at row i |
| WriteLargeTable | write large table to output file, with support for gzip. |
