rmMultiPCRChimera: Remove chimeric reads overlapping multiple primers

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

Finds and removes sets of chimeric read alignments that overlap more than one guide, i.e. that cannot be unambiguously assigned to a single guide.

Usage

rmMultiPCRChimera(readnames, pcrhits, chimera_idxs, ...)

## S4 method for signature 'character,Hits,integer'
rmMultiPCRChimera(readnames, pcrhits,
  chimera_idxs, ..., verbose = TRUE)

Arguments

readnames	A set of read names, used for identifying chimeric read sets
pcrhits	A mapping between indices of reads and a set of pcr primers
chimera_idxs	location of chimeric reads within the bam
...	Additional arguments
verbose	Display information about the chimeras (Default: TRUE)

Value

pcrhits, with chimeric reads mapping to different primers omitted.

Author(s)

Helen Lindsay

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.