find_stutter: Check for PCR stutter between sequences

In ShawHahnLab/microsat: Computational, High-throughput Individual Identification through Microsatellite Profiling

Check for PCR stutter between sequences

Description

Searches a processed STR sample for entries that may be artifacts of PCR stutter from another entry in the sample. This only considers STR-labeled rows and requires a given entry to have counts at most count.ratio_max compared to the candidate "source" entry to be considered stutter. Sequence content is not currently considered, just relative sequence lengths and counts.

Usage

find_stutter(
  sample.data,
  locus_attrs,
  count.ratio_max = cfg("max_stutter_ratio")
)

Arguments

sample.data	data frame of processed sample data.
locus_attrs	data frame of attributes for loci to look for.
count.ratio_max	comparing the currently-checked entry to another entry, this is the highest ratio of counts where an entry will still be considered stutter.

Value

integer vector specifying, for each entry, the row index for another entry that may have produced each entry as a stutter band.

ShawHahnLab/microsat documentation built on Aug. 25, 2023, 11:16 p.m.