pOutlierFinderInOrder: q values for test of neutrality
In whitlock/OutFLANK: Fst outliers with trimming
Description
Usage
Arguments
Value
Description
Calculates q-values for test of neutrality for a list of loci, using input of an inferred degrees of freedom for the chi-square and mean Neutral FST, and returns the results in the same row order as the input
Usage
1
2
pOutlierFinderInOrder(DataList, Fstbar, dfInferred, qthreshold = 0.05,
Hmin = 0.1)
Arguments
DataList
A data frame with a row for each locus, that includes at least a column for $FSTNoCorr. It also helps if there is a column with an identifier for the locus.
Fstbar
Mean Fst (without sample size correction) as inferred from neutral loci or OutFLank
dfInferred
The inferred degrees of freedom of the chi-square distribution describing neutral Fst values.
qthreshold
The threshold False Discovery Rate for calling a locus an outlier ( default = 0.05)
Hmin
The threshold heterozygosity (H) below which loci will be removed
Value
Returns a data frame with the original data, and two new columns appended:
$qvalues the q-value for a locus
$OutlierFlag TRUE if q is less than the qthreshold; FALSE otherwise
$pvalues the p-value for a locus
$pvaluesRightTail the one-sided (right tail) p-value for a locus
whitlock/OutFLANK documentation built on Nov. 5, 2019, 12:09 p.m.
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Description Usage Arguments Value
Description
Calculates q-values for test of neutrality for a list of loci, using input of an inferred degrees of freedom for the chi-square and mean Neutral FST, and returns the results in the same row order as the input
Usage
1 2 | pOutlierFinderInOrder(DataList, Fstbar, dfInferred, qthreshold = 0.05,
Hmin = 0.1)
|
Arguments
DataList |
A data frame with a row for each locus, that includes at least a column for $FSTNoCorr. It also helps if there is a column with an identifier for the locus. |
Fstbar |
Mean Fst (without sample size correction) as inferred from neutral loci or OutFLank |
dfInferred |
The inferred degrees of freedom of the chi-square distribution describing neutral Fst values. |
qthreshold |
The threshold False Discovery Rate for calling a locus an outlier ( default = 0.05) |
Hmin |
The threshold heterozygosity (H) below which loci will be removed |
Value
Returns a data frame with the original data, and two new columns appended:
$qvalues the q-value for a locus
$OutlierFlag TRUE if q is less than the qthreshold; FALSE otherwise
$pvalues the p-value for a locus
$pvaluesRightTail the one-sided (right tail) p-value for a locus
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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