potentialFatherCounts {PolyPatEx} | R Documentation |
Count potential fathers
Description
Count the number of potential fathers detected for each progeny.
Usage
potentialFatherCounts(dataset, mismatches = 0, VLTMin = 1)
Arguments
dataset |
list: a list structure previously output from
|
mismatches |
integer: the maximum allowed number of mismatching loci between candidate and progeny, before the candidate is rejected as a potential father. |
VLTMin |
integer: the minimum number of ‘valid’ loci (loci at which a valid progeny-candidate comparison was possible) required for a candidate to be considered as a potential father. |
Details
Given the output from genotPPE
or
phenotPPE
, potentialFatherCounts
returns,
for each progeny, the number of candidates that are identified as
potential fathers.
To decide whether a given candidate is a potential father to a
given progeny, potentialFatherCounts
uses the quantities
FLCount (the number of loci at which a candidate can provide a
gamete compatible with the progeny) and VLTotal (the number of
loci at which a valid comparison was possible - ‘valid’
loci) that are returned by genotPPE
or
phenotPPE
.
For a candidate to be identified as a potential father of a progeny, there are two criteria to be met:
-
VLTotal >= max(VLTMin,mismatches+1)
, -
FLCount >= VLTotal-mismatches
.
Here, VLTmin
and mismatches
are user-specified
parameters. VLTmin
allows the user to ensure that a
candidate is only considered for potential fatherhood if a
sufficient number of valid loci were available for comparison.
mismatches
allows the user to specify a maximum number of
allowed mismatching loci between progeny and candidate, before
the candidate is rejected as a potential father. Hence the user
may wish to relax the condition that ALL valid loci must match for
a candidate to be regarded as a potential father to a progeny.
Value
A data frame, containing columns Progeny
(progeny
id), Mother
(id of the progeny's mother) and
potentialFatherCount
(the number of potential fathers found
for the given progeny, given the criteria described above).
Author(s)
Alexander Zwart (alec.zwart at csiro.au)
Examples
## 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
gPPE <- genotPPE(gData) ## Perform the exclusion analyses
## Obtain counts of potential fathers of each seedling, allowing a
## single allele mismatch:
pFC <- potentialFatherCounts(gPPE,mismatches=1,VLTMin=2)
## pFC can be viewed or written to file via, e.g. write.csv()