filter_pruned_indexes: Filter away reads which are associated with indexes that have...

In abelew/Rerrrt: Examine RT error rates through sequencing.

Description

At least in theory we should have at least x reads per index before that index is deemed interesting. prune_indexes() creates a list of indexes which have more than this x reads per index and provides it to this. This then removes the rest. Caveat: this filter works on both the mutated and identical data.

Usage

filter_pruned_indexes(
  chng,
  ident,
  wanted_indexes,
  min_reads = 3,
  verbose = FALSE
)

Arguments

chng	Data set of reads which are not identical to the template.
ident	Data set of reads which are identical to the template.
wanted_indexes	Character vector of indexes which have sufficient evidence.
min_reads	Used when verbose to remind us of the number of reads/index.
verbose	Print some information while running?

Value

The remaining reads and a little summary information.

abelew/Rerrrt documentation built on Jan. 15, 2022, 8 a.m.