HAPMAP-format-data: HAPMAP format data

In jiabowang/GAPIT3: GAPIT (Genomic Association and Prediction Integrated Tool)

HAPMAP format data

Description

HAPMAP format data

Details

Genotypic data in HAPMAP format.

Variants are in rows. The first 11 columns contain information about each variant. GAPIT uses columns 1 (variant name; rs), 3 (chromosome; chrom), and 4 (position; pos). Subsequent columns are samples. The example dataset consists of 3093 variants scored for 280 samples.

Examples

 
## Not run: 
myGenoFile <- system.file("extdata", "mdp_genotype_test.hmp.txt.gz", package = "GAPIT3")
myGenotypes  <- read.table(myGenoFile, header = FALSE)
myGenotypes[1:4, 1:11]
myGenotypes[1:4, c(1, 12:20)]

## End(Not run)

jiabowang/GAPIT3 documentation built on March 6, 2025, 2:21 a.m.