DVboostQscore: Generate Q scores for all SVs

In Liuy12/DVboost: Adaptive Variant Filtering using generalized boosted regression models

Generate Q scores for all SVs

Description

After training procedure, DVboost assigns Q scores to each SV based on training on a subset of SVs (only DEL). The higher the Q score, the more likely it is a true SV.

Usage

DVboostQscore(DVb.res, tmp.mtx)

Arguments

DVb.res	output generated by runDVboostwrapper
tmp.mtx	output generated by loadVariants

Value

A data.frame with same format as tmp.mtx with one additional field Qscore

See Also

runDVboostwrapper

Examples

data(ExampleData, package='DVboost')
sample <- 'NA12878'
outdir <- getwd()
tmp.mtx.DEL <- ExampleData[ExampleData$SVType == 'DEL',]
truth.vec <- tmp.mtx.DEL$CNVMAP == 1 | tmp.mtx.DEL$CNVR ==1
is.semi.truth.vec <- as.numeric(truth.vec)
DVb.res <- runDVboostwrapper( var.atr.mtx = tmp.mtx.DEL, var.ID.vec = rownames(tmp.mtx.DEL),
                             is.known.var.vec = is.semi.truth.vec,
                             output.DIR.name = outdir, input.sample.ID=sample, bySVlength=FALSE)
outmat <- DVboostQscore(DVb.res, ExampleData)

Liuy12/DVboost documentation built on Oct. 10, 2024, 10:56 p.m.