filterProfile: 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
)

Value

data.frame with extracted result.

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'.