GAPIT – Genome Association and Prediction Integrated Tool – is an R package that performs GWAS and genome prediction (or selection). This program uses state-of-the-art methods developed for statistical genetics, such as the unified mixed model, EMMA, the compressed mixed linear model, and P3D/EMMAx.

설치 #

Bioconductor를 비롯한 다양한 패키지들이 필요함

$ R
source("https://bioconductor.org/biocLite.R")
biocLite("multtest")
biocLite("chopsticks")

install.packages("gplots")
install.packages("LDheatmap")
install.packages("genetics")
install.packages("EMMREML")
install.packages("scatterplot3d")

library(multtest)
library(gplots)
library(LDheatmap)
library(genetics)
library(EMMREML)
library(compiler)
library(scatterplot3d)

source("http://zzlab.net/GAPIT/gapit_functions.txt")
source("http://zzlab.net/GAPIT/emma.txt")

구동 #

입력파일은 표현형과 유전형 파일 (Trait is simple table text, genotype is HapMap format)

$ head traits.txt
Taxa    EarHT   dpoll   EarDia
sample1     59.5    NaN     NaN
sample2    65.5    59.5    32.21933
sample3    81.13   71.5    32.421
$ head genotypes.hmp.txt
rs  alleles chrom   pos strand  assembly    center  protLSID    assayLSID   panel   QCcode  sample1    sample2    sample3
snp1    C/G    1    12345    +    assembly_id    NaN    NaN    NaN    NaN    NaN    CC    CG    GG
snp1    C/T    1    12345    +    assembly_id    NaN    NaN    NaN    NaN    NaN    TT    CT   CC

R에서 다음처럼 수행하면 한번에 결과 계산

#Step 1: Set working directory and import data
myY <- read.table("traits.txt", head=TRUE)
myG <- read.table("genotypes.hmp.txt" , head=FALSE)
#Step 2: Run GAPIT 
myGAPIT <- GAPIT(Y=myY, G=myG, PCA.total=3)

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