R/ranM.R

In shibiaowan/SHARP: hyperfast and accurate single-cell RNA-Seq data clustering

#' Prepare a random matrix
#'
#' This function is to prepare a random matrix to be used in parallel computation, so that the same random matrix will be applied to different partitions/groups of datasets in the same application of random projection.
#'
#' @param scdata input single-cell expression matrix
#' @param p the dimension to be reduced to
#'
#' @import Matrix
#'
#' @export
ranM <- function(scdata, p, seedn) {
    # for random projection; note scdata: m*n, m is the feature dimensions, n is the
    # sample number; p is the reduced dimension
    m = nrow(scdata)  #the number of features
    n = ncol(scdata)  #number of samples/cells
    # set.seed(123)#a flag to fix the random number
    s = sqrt(m)  #according to the paper 'Very Sparse Random Projection'
    # x0 = sample(c(sqrt(s),0, -sqrt(s)), size= m*p, replace=TRUE, prob=c(1/(2*s), 1
    # - 1/s, 1/(2*s)))
    if (seedn%%1 == 0) {
        # integer
        set.seed(seedn)
        x0 = sample(c(sqrt(s), 0, -sqrt(s)), size = m * p, replace = TRUE, prob = c(1/(2 * 
            s), 1 - 1/s, 1/(2 * s)))
    } else {
        x0 = sample(c(sqrt(s), 0, -sqrt(s)), size = m * p, replace = TRUE, prob = c(1/(2 * 
            s), 1 - 1/s, 1/(2 * s)))
    }
    # return(x)
    x <- Matrix(x0, nrow = m, byrow = TRUE, sparse = TRUE)  #reshape a vector to a sparse matrix
    
    return(x)  #the same format, feature*sample
}