最小二乘法求解替换？

[ShixiangWang]

pracma

lsei 包被下架了，这个包是否可以满足计算需求？

MutationalPatterns::fit_to_signatures
function (mut_matrix, signatures) 
{
    if (dim(mut_matrix)[1] != 96) 
        stop(paste("Mutation count matrix input should have", 
            "dimensions 96 X n samples"))
    if (dim(signatures)[1] != 96) 
        stop("Signatures input should have dimensions 96 X n signatures")
    n_samples = dim(mut_matrix)[2]
    n_signatures = dim(signatures)[2]
    lsq_contribution = matrix(NA, nrow = n_signatures, ncol = n_samples)
    lsq_reconstructed = matrix(NA, nrow = 96, ncol = n_samples)
    for (i in 1:ncol(mut_matrix)) {
        y = mut_matrix[, i]
        lsq = lsqnonneg(signatures, y)
        lsq_contribution[, i] = lsq$x
        lsq_reconstructed[, i] = signatures %*% as.matrix(lsq$x)
    }
    sample_names = colnames(mut_matrix)
    signature_names = colnames(signatures)
    mut_type_names = rownames(signatures)
    colnames(lsq_contribution) = sample_names
    rownames(lsq_contribution) = signature_names
    colnames(lsq_reconstructed) = sample_names
    rownames(lsq_reconstructed) = mut_type_names
    res = list(lsq_contribution, lsq_reconstructed)
    names(res) = c("contribution", "reconstructed")
    return(res)

[ShixiangWang]

lsqnonneg() 这个要和 lsei 包的函数进行一个 Benchmark 测试。