removeAmbiguousAln: Removes rearrangements for which the BLAT-aligned reads do...

In cancer-genomics/trellis: Somatic structural variant analysis

Removes rearrangements for which the BLAT-aligned reads do not pass QC

Description

BLAT records for which the passQC variable is FALSE are removed. The RearrangementList is then subset to include only those rearrangement ids that remain in the BLAT data.frame.

Usage

removeAmbiguousAln(rlist, blat_list)

Arguments

rlist	a RearrangementList
blat_list	a list of data.frame objects, as returned by scoreBlatExperiment

See Also

See blatScores for the approach used to QC BLAT-aligned reads.

Examples

## Not run: 
 library(svovarian)
 dirs <- projectOvarian(rootname="OvarianData2")
 if(FALSE){
 ## A BLAT-filtered RearrangementList
 ##saved_result <- readRDS(file.path(dirs[["unit_test"]], "blat_filtered.rds"))
 ##tag_list <- readRDS(file.path(dirs[["unit_test"]], "tag_seqs.rds"))
 blat <- scoreBlatExperiment(tag_list, dirs)
 blat_list <- blat["CGOV2T"]

 rlist <- readRDS(file.path(dirs[["rear:filter"]], "CGOV2T.rds"))
 rlist <- list(CGOV2T=rlist)
 ## Another BLAT-filtered RearrangementList created by 'removeAmbigousAln'
 filtered_rlist <- removeAmbiguousAln(rlist, blat_list)
 print(filtered_rlist)
 }

## End(Not run)

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.