Calculate Concordance.

Description

Calculates concordance and discordance for profiles in multiple datasets.

Usage

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calculateConcordance(data, kit.name = NA, no.marker = "NO MARKER",
  no.sample = "NO SAMPLE", delimeter = ",", list.all = FALSE,
  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'.

list.all

logical TRUE to return missing samples.

debug

logical indicating printing debug information.

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).

Value

list of data.frames (discordance table, and pair-wise comparison).

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