filterProfile: Filter Profile
Description
Filter peaks from profiles.Usage
filterProfile(data, ref, add.missing.loci = FALSE, keep.na = FALSE,
ignore.case = TRUE, invert = FALSE, 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.
invert
logical TRUE filter peaks NOT matching the reference.
debug
logical indicating printing debug information.
Value
- data.frame with extracted result.
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).
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'.