ReadIntList: Load hardcalls for multiple variants as an integer matrix.
In pgenlibr: PLINK 2 Binary (.pgen) Reader
ReadIntList R Documentation
Load hardcalls for multiple variants as an integer matrix.
Description
This function treats the data as diploid; you can divide by 2, and then
treat 0.5 as NA, if it's actually haploid.
Usage
ReadIntList(pgen, variant_subset)
Arguments
pgen
Object returned by NewPgen().
variant_subset
Integer vector containing 1-based indexes of variants
to load.
Value
Integer matrix, where rows correspond to samples, columns
correspond to variant_subset, and values are in {0, 1, 2, NA} indicating
the number of hardcall ALT allele copies. For multiallelic variants, all
ALT alleles are combined.
pgenlibr documentation built on April 3, 2025, 6:21 p.m.
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| ReadIntList | R Documentation |
Load hardcalls for multiple variants as an integer matrix.
Description
This function treats the data as diploid; you can divide by 2, and then treat 0.5 as NA, if it's actually haploid.
Usage
ReadIntList(pgen, variant_subset)
Arguments
pgen |
Object returned by NewPgen(). |
variant_subset |
Integer vector containing 1-based indexes of variants to load. |
Value
Integer matrix, where rows correspond to samples, columns correspond to variant_subset, and values are in {0, 1, 2, NA} indicating the number of hardcall ALT allele copies. For multiallelic variants, all ALT alleles are combined.
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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