filterProfile {strvalidator}

Filter Profile

Description

Filter peaks from profiles.

Usage

filterProfile(
  data,
  ref = NULL,
  add.missing.loci = FALSE,
  keep.na = FALSE,
  ignore.case = TRUE,
  exact = FALSE,
  word = FALSE,
  invert = FALSE,
  sex.rm = FALSE,
  qs.rm = FALSE,
  kit = NULL,
  filter.allele = TRUE,
  debug = FALSE
)

Arguments

data

data frame with genotype data in 'slim' format.

ref

data frame with reference profile in 'slim' format.

add.missing.loci

logical. TRUE add loci present in ref but not in data. Overrides keep.na=FALSE.

keep.na

logical. FALSE discards NA alleles. TRUE keep loci/sample even if no matching allele.

ignore.case

logical TRUE ignore case.

exact

logical TRUE use exact matching of sample names.

word

logical TRUE adds word boundaries when matching sample names.

invert

logical TRUE filter peaks NOT matching the reference.

sex.rm

logical TRUE removes sex markers defined by 'kit'.

qs.rm

logical TRUE removes quality sensors defined by 'kit'.

kit

character string defining the kit used. If NULL automatic detection will be attempted.

filter.allele

logical TRUE filter known alleles. FALSE increase the performance if only sex markers or quality sensors should be removed.

debug

logical indicating printing debug information.

Details

Filters out the peaks matching (or not matching) specified known profiles from typing data containing 'noise' such as stutters. If 'ref' does not contain a 'Sample.Name' column it will be used as reference for all samples in 'data'. The 'invert' option filters out peaks NOT matching the reference (e.g. drop-in peaks). Sex markers and quality sensors can be removed. NB! add.missing.loci overrides keep.na. Returns data where allele names match/not match 'ref' allele names. Required columns are: 'Sample.Name', 'Marker', and 'Allele'.

Value

data.frame with extracted result.