setFilters: Set filters for a Tomahawk output records

In mklarqvist/rtomahawk: Tools for computing, querying and storing linkage-disequilibrium data

Description

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.

Usage

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", ...)

Slots

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.

Author(s)

Marcus D. R. Klarqvist <[e-mail]> | <https://mdrk.me>

See Also

twk_index, twk_data, twk_filter, and twk

mklarqvist/rtomahawk documentation built on May 16, 2019, 5:01 a.m.