CollapseGeno: Collapse Variants
In AllelicSeries: Allelic Series Test
CollapseGeno R Documentation
Collapse Variants
Description
Collapse variants with minor allele counts below the min_mac threshold
into an aggregated variant, separately within each variant category. Note
that the ordering of the variants will change, and that collapsing does not
guarantee that the resulting aggregate variant will itself have a
MAC greater than or equal to min_mac.
Usage
CollapseGeno(anno, geno, min_mac = 11)
Arguments
anno
(snps x 1) annotation vector with integer values in 1 through
the number of annotation categories L.
geno
(n x snps) genotype matrix.
min_mac
Minimum minor allele count (MAC) for retention as an
individual variant. Variants with a MAC strictly less than the minimum
MAC will be collapsed into an aggregated variant, separately within
each annotation category.
Value
List containing the collapsed genotypes geno and corresponding
annotations anno, plus a data.frame vars specifying which variants
were collapsed within each annotation category.
AllelicSeries documentation built on April 3, 2025, 7:46 p.m.
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| CollapseGeno | R Documentation |
Collapse Variants
Description
Collapse variants with minor allele counts below the min_mac threshold
into an aggregated variant, separately within each variant category. Note
that the ordering of the variants will change, and that collapsing does not
guarantee that the resulting aggregate variant will itself have a
MAC greater than or equal to min_mac.
Usage
CollapseGeno(anno, geno, min_mac = 11)
Arguments
anno |
(snps x 1) annotation vector with integer values in 1 through the number of annotation categories L. |
geno |
(n x snps) genotype matrix. |
min_mac |
Minimum minor allele count (MAC) for retention as an individual variant. Variants with a MAC strictly less than the minimum MAC will be collapsed into an aggregated variant, separately within each annotation category. |
Value
List containing the collapsed genotypes geno and corresponding
annotations anno, plus a data.frame vars specifying which variants
were collapsed within each annotation category.
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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