R/filtering.R

In eprifti/momr: Mining Metaomics Data (MetaOMineR)

#' \code{filterListGenebags}
#' @title filterListGenebags
#' @description This function filters a list of mgs with gene_id >= a given mgs gene number.
#' @author Emmanuelle Le Chatelier
#' @param list.genebags : a list of genebags that needs to be filtered
#' @param size.min : the minimal size threshold above which mgs are selected, default 0
#' @param size.max : the maximal size threshold above which mgs are selected, default 15000
#' @return a list of selected genebags with their original elements (usually geneids)
#' @note This is the former filterListMGS function
filterListGenebags <- function(list.genebags,
                               size.min = 0,
                               size.max = 15000) {
  if (!is.list(list.genebags)) {
    stop("Error! this is not a list")
  }
  res <- list.genebags[as.numeric(summary(list.genebags)[, 1]) >= size.min &
                         as.numeric(summary(list.genebags)[, 1]) <= size.max]
  return(res)
}


#' \code{filterMat}
#' @title filterMat
#' @description This function filters a matrix (mat) based on the rate of positive value (filt)
#' in each individual under a given degree of presence (filt), all sparse values are put to 0.
#' @author Edi Prifti & Emmanuelle Le Chatelier
#' @param mat : matrix of counts
#' @param filt : filtering threshold in percentage
#' @return a cleaned matrix
filterMat <- function(mat, filt = 0) {
  if (!is.matrix(mat)) {
    stop("Error! only a matrix can be provided ")
  }
  tmp <- mat
  tmp[, colSums(mat != 0) < round(nrow(mat) * filt / 100)] <- 0
  return(tmp)
}

#' End of section and file