vcfppR (version 0.8.2)

subset.vcftable: Subset a vcftable object

Description

S3 method for subsetting vcftable objects by rows (variants) and columns (fields). Allows filtering variants based on logical conditions and selecting specific fields.

Usage

# S3 method for vcftable
subset(x, subset, select, drop = FALSE, ...)

Value

A vcftable object with the selected variants and fields.

Arguments

x

a vcftable object returned by vcftable

subset

logical expression indicating variants (rows) to keep. The expression is evaluated in the context of the vcftable object, allowing direct reference to fields like chr, pos, ref, alt, qual, etc. Missing values are treated as FALSE.

select

expression indicating which fields (columns) to select. If omitted, all fields except samples are selected. Note: the samples field is always kept and cannot be selected/deselected.

drop

logical. If TRUE, the result is coerced to the lowest possible dimension. Passed to the [ operator when subsetting. Default FALSE.

...

Currently not used but can avoid S3 generic consistency warnings

Author

Zilong Li

Examples

library('vcfppR')
vcffile <- system.file("extdata", "raw.gt.vcf.gz", package="vcfppR")
res <- vcftable(vcffile, "chr21:1-5050000")

# Subset by quality score
high_qual <- subset(res, qual > 100)

# Subset by position and select specific fields
region_subset <- subset(res, pos >= 5000000 & pos <= 5010000,
                        select = c(chr, pos, ref, alt))

region_subset <- subset(res, pos >= 5000000 & pos <= 5030400,
                        select = c(chr, pos, ref, alt))

# Subset SNPs (REF and ALT are single nucleotides)
snps <- subset(res, nchar(ref) == 1 & nchar(alt) == 1)