Identify 'foreign' alleles (alleles present in progeny, but not in
parents or other non-parental adults). Note that
foreignAlleles does not distinguish between
populations as indicated by the
popn column of the allele
data frame: the preprocessed allele data set
returned by either
A list, containing two data frames. Data frame
byLocus summarises the foreign alleles found at each locus.
byProgenyLocus summarises the same alleles by
progeny and locus. In this latter data frame, the code
P.missing indicates no alleles were present in the progeny
at this locus.
Alexander Zwart (alec.zwart at csiro.au)
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## Using the example dataset 'FR_Genotype': data(FR_Genotype) ## Since we did not load this dataset using inputData(), we must ## first process it with preprocessData() before doing anything ## else: gData <- preprocessData(FR_Genotype, numLoci=7, ploidy=4, dataType="genotype", dioecious=TRUE, mothersOnly=TRUE) head(gData) ## Checked and Cleaned version of FR_Genotype fAlleles <- foreignAlleles(gData) ## View foreign alleles detected at each locus: fAlleles$byLocus ## View foreign alleles detected in each progeny, at each locus: fAlleles$byProgenyLocus ## Both of these objects are data frames, hence can be written to file ## via, e.g., write.csv().
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