calculateConcordance Compares profiles in multiple datasets.
Usage
calculateConcordance(data, kit.name = NA, no.marker = "NO MARKER",
no.sample = "NO SAMPLE", delimeter = ",", debug = FALSE)
Arguments
data
list of data frames in 'slim' format with at least columns
'Sample.Name', 'Marker', and 'Allele'.
kit.name
character vector for DNA typing kit names in same order and
of same lengths as data sets in 'data' list. Default is NA in which case
they will be numbered.
no.marker
character vector for string when marker is missing.
no.sample
character vector for string when sample is missing.
delimeter
character to separate the alleles in a genotype.
Default is comma e.g '12,16'.
debug
logical indicating printing debug information.
Value
list of data.frames (discordance table, and pair-wise comparison).
Details
Takes a list of datasets as input. It is assumed that each unique
sample name represent a result originating from the same source DNA and
thus is expected to give identical DNA profiles. The function first compare
the profiles for each sample across datasets and lists discordant results.
Then it performs a pair-wise comparison and compiles a concordance table.
The tables are returned as two data frames in a list.
NB! Typing and PCR artefacts (spikes, off-ladder peaks, stutters etc.)
must be removed before analysis.
NB! It is expected that the unique set of marker names across a dataset is
present in each sample for that dataset (a missing marker is a discordance).