Description Usage Slots Author(s) See Also
Some additional details about this S4 generic and its methods. The extra blank line between this section and the title is critical for roxygen2 to differentiate the title from the description section.
1 2 3 4 5 6 7 8 9 10 11 | setFilters(x = "ANY", flagInclude = "numeric",
flagExclude = "numeric", minD = "numeric", maxD = "numeric",
minDprime = "numeric", maxDprime = "numeric", minR = "numeric",
maxR = "numeric", minR2 = "numeric", maxR2 = "numeric",
minP = "numeric", maxP = "numeric", minP1 = "numeric",
maxP1 = "numeric", minP2 = "numeric", maxP2 = "numeric",
minQ1 = "numeric", maxQ1 = "numeric", minQ2 = "numeric",
maxQ2 = "numeric", minChiSqFisher = "numeric",
maxChiSqFisher = "numeric", minChiSqModel = "numeric",
maxChiSqModel = "numeric", upperOnly = "logical",
lowerOnly = "logical", ...)
|
flagInclude
Integer representing FLAGs to include.
flagExclude
Integer representing FLAGs to exclude.
minD
Smallest Lewontin D value.
maxD
Largest Lewontin D value.
minDprime
Smallest scaled Lewontin D value.
minDprime
Largest scald Lewontin D value.
minR
Smallest Pearson's correlation coefficient value.
minR
Largest Pearson's correlation coefficient value.
minR2
Smallest scaled Pearson's correlation coefficient value.
minR2
Largest scaled Pearson's correlation coefficient value.
minP
Smallest Fisher's exact test P-value.
minP
Largest Fisher's exact test P-value.
minP1
Smallest count of REF-REF.
minP1
Largest count of REF-REF.
minP2
Smallest count of REF-ALT.
minP2
Largest count of REF-ALT.
minQ1
Smallest count of ALT-REF.
minQ1
Largest count of ALT-REF.
minQ2
Smallest count of ALT-ALT.
minQ2
Largest count of ALT-ALT.
minChiSqFisher
Smallest Chi-squared test of the 2x2 haplotype table.
minChiSqFisher
Largest Chi-squared test of the 2x2 haplotype table.
minChiSqModel
Smallest Chi-squared test of the 4x4 genotype table.
minChiSqModel
Largest Chi-squared test of the 4x4 genotype table.
upperOnly
Logical flag indicating whether upper triangular values only should be kept.
lowerOnly
Logical flag indicating whether lower triangular values only should be kept.
Marcus D. R. Klarqvist <mk819@cam.ac.uk> | <https://mdrk.me>
twk_index
, twk_data
,
twk_filter
, and twk
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