software: Identify Software Used for Calling Genotypes in a VCF

In ploidyverse/ploidyverseClasses: Accessors and Utilities for VCFs in the Ploidyverse

Description

The software function retrieves information about the software used to generate genotype calls present in a ploidyverse VCF. The corresponding assignment function can be used to add the same data to a VCF object.

Usage

software(object)

software(object) <- value

Arguments

object	A VCF object.
value	A named character vector, named list, or data frame. The names (or column names) Software, Version, Model, and Description must be present. The name ID must also be present if multiple values are provided for each field. If value is a DataFrame, it is allowed to use row names instead of the ID field. Any additional named items will also be retained in the output, allowing for custom fields.

Value

software returns a DataFrame containing information about the software used for genotype calling.

software<- stores software metadata in a DataFrame in meta(header(object))$ploidyverse.

Author(s)

Lindsay V. Clark

See Also

markValidity

Examples

## Not run: 
# To add software information to a new VCF
software(myvcf) <- c(Software = "polyRAD", Version = "1.1", Model = "IteratePopStruct",
                     Description = "Just some genotypes")
software(myvcf)

# To add additional software information, without overwriting
software(myvcf) <- rbind(software(myvcf),
                         DataFrame(row.names = "Phasing",
                                   Software = "Beagle",
                                   Version = "5000",
                                   Model = "spiffy polyploid model",
                                   Description = "Imputation with Beagle"))

## End(Not run)

ploidyverse/ploidyverseClasses documentation built on May 25, 2019, 2:21 p.m.