query_gt: Query the gt slot

In vcfR: Manipulate and Visualize VCF Data

Query the gt slot

Description

Query the 'gt' slot of objects of class vcfR

Usage

is.polymorphic(x, na.omit = FALSE)

is.biallelic(x)

Arguments

x	an object of class vcfR
na.omit	logical to omit missing data

Details

The function is_polymorphic returns a vector of logicals indicating whether a variant is polymorphic. Only variable sites are reported in vcf files. However, once someone manipulates a vcfR object, a site may become invariant. For example, if a sample is removed it may result in a site becoming invariant. This function queries the sites in a vcfR object and returns a vector of logicals (TRUE/FALSE) to indicate if they are actually variable.

The function is_bialleleic returns a vector of logicals indicating whether a variant is biallelic. Some analyses or downstream analyses only work with biallelic loci. This function can help manage this.

Note that is_bialleleic queries the ALT column in the fix slot to count alleles. If you remove samples from the gt slot you may invalidate the information in the fix slot. For example, if you remove the samples with the alternate allele you will make the position invariant and this function will provide inaccurate information. So use caution if you've made many modifications to your data.

See Also

extract.gt

vcfR documentation built on May 29, 2024, 10:57 a.m.