comparison mutational_patterns.R @ 13:6741b819cc15 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 372eb902f528baa8b5465b83d992a1d146343dfe"

12:7954f0d3517f

    # export relative contribution matrix
    if (!is.na(opt$sig_contrib_matrix)) {
        output_table <- t(fit_res$contribution)/rowSums(t(fit_res$contribution))
        colnames(output_table) <- paste0("s", colnames(output_table))
        if (length(levels(factor(levels_table$level))) > 1) {
            output_table <- data.frame(sample=worklist$sample, output_table)
            } else {
        output_table <- data.frame(sample=rownames(output_table), output_table)
        }
        write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = F, row.names = F)
    }

13:6741b819cc15

    # export relative contribution matrix
    if (!is.na(opt$sig_contrib_matrix)) {
        output_table <- t(fit_res$contribution)/rowSums(t(fit_res$contribution))
        colnames(output_table) <- paste0("s", colnames(output_table))
        if (length(levels(factor(levels_table$level))) > 1) {
            output_table <- data.frame(sample=paste0(metadata_table[metadata_table$element_identifier==colnames(fit_res$contribution),
                                                                    3], "-", colnames(fit_res$contribution) ),
                                       output_table)
            } else {
        output_table <- data.frame(sample=rownames(output_table), output_table)
        }
        write.table(output_table, file = opt$sig_contrib_matrix, sep = "\t", quote = F, row.names = F)
    }