R/maaslinformat.R

In zellerlab/siamcat: Statistical Inference of Associations between Microbial Communities And host phenoTypes

#!/usr/bin/Rscript
### SIAMCAT - Statistical Inference of Associations between
### Microbial Communities And host phenoTypes R flavor EMBL
### Heidelberg 2012-2018 GNU GPL 3.0

#' @title create a MaAsLin input file from SIAMCAT object
#'
#' @description This function creates a MaAsLin merged PCL single input file
#' from SIAMCAT object
#'
#' @param siamcat object of class \link{siamcat-class}
#'
#' @param filename name of the input file to which data will be save
#'
#' @keywords internal
#'
#' @return nothing but data is written to a file
#'
#' @export
#'
#' @encoding UTF-8
#'
#' @examples
#'
#' data(siamcat_example)
#' siamcat.to.maaslin(siamcat_example)
siamcat.to.maaslin <- function(siamcat, filename="siamcat_output.pcl") {
    feat   <- get.orig_feat.matrix(siamcat)
    label  <- label(siamcat)
    meta   <- NULL
    if(!is.null(meta(siamcat))) meta   <- t(meta(siamcat))
    labelD <- label$label
    labelD[label$p.idx] <- label$p.lab
    labelD[label$n.idx] <- label$n.lab

    results <- rbind(labelD,
                        meta,
                        colnames(feat),
                        feat)

    rownames(results) <- c("label",
                            rownames(meta),
                            "sample_id",
                            rownames(feat))

    write.table(results,
                file = filename,
                quote = FALSE,
                sep = '\t',
                row.names = TRUE,
                col.names = FALSE)
}