rmMultiPCRChimera: Remove chimeric reads overlapping multiple primers

Description Usage Arguments Value Author(s)

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

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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.