R/getsolvedmatrix_with_permutation_cell_label.R

In scMAGeCK: Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

# function definitions ##### version: 02-22-2019 should sync from the version in macbook:
# /Users/weili/Dropbox/work/cropseq/Shendure/nmeth18/multiple_guides_function.R


getsolvedmatrix_with_permutation_cell_label <- function(Xm, Ym, lambda = 0.01, npermutation = 1000) {
    Amat_ret = getsolvedmatrix(Xm, Ym, lambda = lambda)
    Amat_ret_higher = matrix(rep(0, ncol(Amat_ret) * nrow(Amat_ret)), nrow = nrow(Amat_ret))
    rownames(Amat_ret_higher) = rownames(Amat_ret)
    colnames(Amat_ret_higher) = colnames(Amat_ret)
    # permute N times randomly shuffle cell labels
    for (npm in 1:npermutation) {
        if (npm%%100 == 0) {
            message(paste("Permutation:", npm, "/", npermutation, "..."))
        }
        cells_shu = sample(rownames(Ym), nrow(Ym))
        Xm_s = Xm[cells_shu, ]
        Ym_s = Ym  # [cells_shu,]
        rownames(Ym_s) = cells_shu
        Amat_random = getsolvedmatrix(Xm_s, Ym_s, lambda = lambda)
        
        Amat_ret_higher = Amat_ret_higher + (abs(Amat_random) > abs(Amat_ret)) * 1
        # browser()
    }
    Amat_ret_higher = Amat_ret_higher/npermutation
    return(list(Amat_ret, Amat_ret_higher))
}
TRUE