Man pages for kindlychung/CollapsABEL
An R package for quantitative CDH analysis

appendEnvMerge two enviroments
appendFromPlinkOutRead a PLINK assoc file into a QCDH info hub
bedcollinfoCollect info on shifted bed files
bedcollrShift bed files
catmatPrint out a matrix, in a clean format
checkBinaryTraitCheck whether a trait is binary
cleanByChrPvalsBonferExtract relevant SNP out of the QCDH data hub
cleanSnpNamesClean up SNP names for building linear models in R
collapseGenotype collapsing functions
contrastPlotContrast QCDH p values with single-SNP p values
dbgtriggerGetting or setting a local boolean variable for debugging...
getNshiftStrExtract shift number (as a string) from a shifted bed...
getPlinkParamGet a list of parameters for passing to plinkr
getstemGet the stem of a bed filename.
gwasA pure R implementation of GWAS
plinkcollrApply plinkr to multiple files
plinkrA wrapper for plink
qcdhRoutineQCDH routine 2
readcollRead PLINK assoc files int matrices and store them in the...
rep_datBatch version of the 'rep_models' function:
rep_modelsGiven a pair of SNPs, fit a model using single and collapsed...
routine1QCDH routine 1
shiftDataByColShift columns of a matrix
snpPairLookin.quantLook into a pairs of SNPs
taskAnalyzeAnalyze shifted bed files
taskBedsPlinkOutPrepare shifted bed files for current task.
taskinfoPrepare paths and filenames for the task
updateMinPvalsCalculate minial p values for QCDH
kindlychung/CollapsABEL documentation built on May 18, 2017, 7:49 p.m.