tibble_to_gwaa: Convert tibble with genotypes along with a vector of...

Description Usage Arguments Details Value Author(s)

View source: R/tibble_to_gwaa.R

Description

Convert tibble with genotypes along with a vector of phenotypes to GenABEL internal raw gwaa.data format.

Usage

1
tibble_to_gwaa(x, sex, trait, progress = 1)

Arguments

x

tibble with genotypes as described in the Details section

sex

a vector of sex values: 0 - female, 1 - male

trait

a vector of trait values

progress

report progress every N individuals

Details

Convert a tibble with the following shape: test_data <- tibble( chr = c(1), pos = c(1001,1002,1005,1017), snp = c('snp1', 'snp2', 'snp3', 'snp4'), strand = c('u'), ind1 = c(0,1,1,2), id2 = c(2,NA,1,1), john = c(0,0,1,0), jill = c(1,1,1,2), elon = c(2,0,NA,1) where columns from 5 to the end are genotypes and names of the columns are sample/individual names. the 'snp' column contains names of the snp markers, 'chr' is an integer denoting chromosome, 'pos' is the genome-wide position (or chromosome-based position), 'strand' is currently ignored, but required as a separate column. Genotypes have to be coded as counts of the MINOR ALLELE: AA - 0, Aa - 1 and aa - 2, NA values are allowed.

Value

gwaa.data-class object

Author(s)

Marcin Kierczak <marcin.kierczak_NO_SPAM_scilifelab.se>


NBISweden/a_johansson_2020 documentation built on April 18, 2021, 1:09 a.m.