get_vcf_group_info

associate samples with group info based on "strata" file

"strata" is a tsv file with 2+ columns, with 2 columns name id and pop

Usage

get_vcf_group_info(vcf, data_path, strt = "strata", grps = "groups")

Arguments

vcf

-> vcfR object

data_path

-> path to data (where strata and groups are located)

strt

-> file with 2+ columns, one id column and one pop column (tsv file, header = TRUE)

grps

-> one column file listing groups to include, column name pop (header = TRUE)

Value

list of factors of sample-to-group assignments and groups

Details

This function creates list of factors of sample-to-group assignments and groups based on a strata and group file

Author

Tomas Hrbek July 2022

Examples

get_vcf_group_info(vcf = my_vcf, data_path = data_path, strt = "strata", grps = "groups")
#> Error: object 'my_vcf' not found
get_vcf_group_info(my_vcf, data_path, strt = "strata", grps = "groups")
#> Error: object 'my_vcf' not found
get_vcf_group_info(my_vcf, data_path)
#> Error: object 'my_vcf' not found