Man pages for Halvee/rvatk
Rare Variant Analysis Toolkit

AddLooMafColadd a leave-one-out minor allele freq. column with values to...
ApplyThresholdsubset on input table on a user defined condition.
BurdenTestperform a case/control burden test on aggregated rare variant...
CollapsingMatrixInitinitializes data frame with discrete genes as rows and...
CollapsingMatrixReadread in a collapsing matrix file from file (gzip detection...
CollapsingMatrixRecoderecode a collapsing matrix using a qualvar data frame.
CollapsingMatrixShrinktake a subset of collapsing matrix where each gene has at...
CollapsingMatrixWritewrite collapsing matrix to output filename (gzipping...
GetAlleleCountsfor input variant calls and genotypes, return genotype...
PlinkBedAlleleSumget sum of allele counts across plinkbed for user-defined...
PlinkBedCallsreturn variant calls per sample that match user-defined...
PlinkBedGtsTransformreturn genotypes from plinkbed into counts that are expected.
PlinkBedInitfunctions for working with plinkbed, a snpMatrix object...
PlinkBedSubsetsubset plinkbed on user-defined set of samples and variants.
PlinkBedToQualvarconvert plinkbed data to qualvar data frame and return.
ProcessStringconvert process input string into a form more agreeable with...
QualvarReadread a file of format qualvar into a qualvar dataframe.
QualvarSubsetsubset qualvar dataframe on user-defined sets of samples and...
QualvarToCollapsingMatrixconvert qualvar dataframe to collapsing matrix data frame.
ReadConditionFileread in a .condition file, where each line represents...
ReadGenesetsFileread genesets file to a list of genesets.
ReadLargeTableread a large table (can be gzipped and/or GB in size) into a...
ReadListFileread in a file where each line is a seperate entry into a...
SamplepedIidFidListtable sampleped data frame and get list of individual ID ->...
StringToSetsplit string to vector
TblCndSubsetsubset on table based on rows in condition data frame.
UpdateTableupdate input table with values of res.list at row i
WriteLargeTablewrite large table to output file, with support for gzip.
Halvee/rvatk documentation built on May 6, 2019, 10:55 p.m.