Nothing
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#' To perform GWAS with GLM and MLM model and get the P value of SNPs
#'
#' Build date: Aug 30, 2016
#' Last update: May 25, 2017
#'
#' @author Lilin Yin and Xiaolei Liu
#'
#' @param phe phenotype, n * 2 matrix
#' @param geno Genotype in numeric format, pure 0, 1, 2 matrix; m * n, m is marker size, n is population size
#' @param CV Covariance, design matrix(n * x) for the fixed effects
#' @param cpu number of cpus used for parallel computation
#' @param verbose whether to print detail.
#'
#' @return m * 2 matrix, the first column is the SNP effect, the second column is the P values
#' @export
#'
#' @examples
#' \donttest{
#' phePath <- system.file("extdata", "07_other", "mvp.phe", package = "rMVP")
#' phenotype <- read.table(phePath, header=TRUE)
#' idx <- !is.na(phenotype[, 2])
#' phenotype <- phenotype[idx, ]
#' print(dim(phenotype))
#' genoPath <- system.file("extdata", "06_mvp-impute", "mvp.imp.geno.desc", package = "rMVP")
#' genotype <- attach.big.matrix(genoPath)
#' genotype <- deepcopy(genotype, cols=idx)
#' print(dim(genotype))
#'
#' glm <- MVP.GLM(phe=phenotype, geno=genotype, cpu=1)
#' str(glm)
#' }
MVP.GLM <-
function(
phe,
geno,
CV=NULL,
cpu=1,
verbose=TRUE
){
n <- ncol(geno)
m <- nrow(geno)
ys <- as.numeric(as.matrix(phe[,2]))
if(!is.big.matrix(geno)) stop("genotype should be in 'big.matrix' format.")
if(sum(is.na(ys)) != 0) stop("NAs are not allowed in phenotype.")
if(nrow(phe) != ncol(geno)) stop("number of individuals not match in phenotype and genotype.")
if(is.null(CV)){
X0 <- matrix(1, n)
}else{
CV.index <- apply(CV, 2, function(x) length(table(x)) > 1)
CV <- CV[, CV.index, drop=FALSE]
X0 <- cbind(matrix(1, n), CV)
}
X0 <- as.matrix(X0)
iX0X0 <- MASS::ginv(crossprod(X0))
logging.log("scanning...\n", verbose = verbose)
mkl_env({
results <- glm_c(y = ys, X = X0, iXX = iX0X0, geno@address, verbose = verbose, threads = cpu)
})
return(results[, c(1, 2, ncol(results))])
}#end of MVP.GLM function
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.