R/batch_t_test.R

In jmzeng1314/humanid: gene id annotation

#' do batch t.test for a matrix
#'
#'

#' @param dat    Matrix with microarray expression values.
#' @param group_list Factors for two groups that are tested for differential expression.
#' @return a data.frame just like topTable
#' @export
#' @keywords batch_t_test
#' @examples
#' #'  batch_t_test()
#'
#'
batch_t_test <- function(dat = matrix(rnorm(300), 30, 10), group_list = factor(c(rep(1, 5), rep(2, 5)))) {
    
    group1 = which(group_list == levels(group_list)[1])
    group2 = which(group_list == levels(group_list)[2])
    dat1 = dat[, group1]
    dat2 = dat[, group2]
    dat = cbind(dat1, dat2)
    
    library(pi0)
    pvals = matrix.t.test(dat, 1, length(group1), length(group2))
    p.adj = p.adjust(pvals, method = "BH")
    avg_1 = rowMeans(dat1)
    avg_2 = rowMeans(dat2)
    FC = avg_2/avg_1
    results = cbind(avg_1, avg_2, FC, pvals, p.adj)
    rownames(results) = rownames(dat)
    results = as.data.frame(results)
    return(results[order(results$pvals), ])
    
}