R/gemini_prepare_input.R

In gemini: GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

#' Prepare input before Model creation
#'
#' @description This is an internal function to GEMINI, allowing for data cleanup and preprocessing before a Model object is created. This removes any gene pairs targeting the same gene twice, and removes any empty samples/replicates.
#'
#' @param Input An object of class gemini.input
#' @param gene.columns a character vector of length(2)
#' @param sample.col.name a character indicating the name of the sample column (default = "samplename")
#'
#' @return a (prepared) gemini.input object
#' 
#' @examples 
#' data("Input", package = "gemini")
#' Input %<>% gemini_prepare_input(gene.columns = c("U6.gene", "H1.gene"))
#' 
#' @importFrom dplyr filter
#' @importFrom dplyr select
#' 
#' @export
#'

gemini_prepare_input <-
    function(Input, gene.columns, sample.col.name = "samplename") {
        LFC = "LFC"
        newInput <- list()
        class(newInput) <- base::union(class(Input), "gemini.input")
        
        dups <-
            apply(Input$guide.pair.annot[, gene.columns], 1, function(x)
                any(duplicated(x)))
        newInput[["counts"]] <-
            Input$counts[!dups, colSums(!is.na(Input$counts)) != 0]
        newInput[["replicate.map"]] <- Input$replicate.map %>%
            dplyr::filter(colSums(!is.na(Input$counts)) != 0) %>%
            dplyr::select(c("colname", sample.col.name, "TP"))
        newInput[["guide.pair.annot"]] <- Input$guide.pair.annot %>%
            dplyr::filter(!dups) %>%
            dplyr::select(c("rowname", gene.columns))
        if (LFC %in% names(Input)) {
            newInput[["LFC"]] <-
                data.matrix(Input[[LFC]][!dups, unique(newInput$replicate.map$sample[newInput$replicate.map$TP ==
                                                                                         "LTP"])])
            colnames(newInput[["LFC"]]) <- colnames(Input[[LFC]])
        }
        return(newInput)
    }