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. |
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