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README.md

GAMMAR

Generalized Renown Analysis of Molecular variance for Mixed model Analysis R package

Usage

Step 1. Install and load the package

library(devtools)
install_github("2eding/GAMMAR")
library(GAMMAR)

Step 2. Input data

X <- as.matrix(data.table::fread("X_rightdim.txt"))
Y <- as.matrix(data.table::fread("Y_rightdim.txt"))

  • data.table::fread <= This package is useful for input large data
  • X_rightdim.txt is snp data
  • Y_rightdim.txt is gene expression data

Step 3. Calculate the kinship

K <- Kinship(X)

Step 4. Calculate the variance components

VC <- varComp(K, Y, X)

Step 5. Run GRAMMAR

run <- run_grammar(K, Y, X, VC, max_itr = 4, num.parallel = 4, outPath = "./test/", outName = "result.txt")

Publication

http://doi.org/10.5391/IJFIS.2020.20.3.1

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Generalized Renown Analysis of Molecular variance for Mixed model Analysis R package

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