R/in_mds_for_crosomics.R

In omicRexposome: Exposome and omic data associatin and integration analysis

in_mds_for_crosomics <- function(mds, na.rm = FALSE, verbose=FALSE, warnings=TRUE) {
    ## --------------------------------------------------------------------- ##
    ## CREATE LIST OF TABLES IN BASE OF THE TYPE OF DATA
    dta_list <- list()
    fdt_list <- list()

    ii <- 1
    for(name in names(mds)) {
        set <- mds[[name]]
        if(class(set) == "SnpSet")  {
            if(verbose) {
                message("Creating table for SnpSet.")
            }

            dta <- t(snpToContinuous(set, verbose))
            rownames(dta) <- Biobase::sampleNames(set)
            colnames(dta) <- Biobase::featureData(set)
            fdt <- Biobase::fData(set)[colnames(dta), ]

            if(sum(is.na(dta)) != 0 & !na.rm) {
                stop("Table SnpSet contains NA values.")
            } else if(sum(is.na(dta)) != 0 & na.rm) {
                if(verbose) {
                    message("Removing SNPs with missing data.")
                }
                onc <- ncol(dta)
                dta <- dta[ , colSums(dta) == 0]
                if(verbose | warnings) {
                    r <- onc - ncol(dta)
                    warning("Removed ", r, " (", round(r/onc * 100, 2), "%) SNPs from original SnpSet.")
                }
                rm(onc)

                fdt <- Biobase::fData(set)[colnames(dta), ]
            }

            dta_list[[ii]] <- dta
            fdt_list[[ii]] <- fdt
        } else if (class(set) == "ExposomeSet") {
            if(verbose) {
                message("Creating table for ExposomeSet")
            }
            dta <- rexposome::expos(set)
            if(verbose | warnings) {
                warning("Factor exposures will be discarded.")
            }
            sel <- rexposome::exposureNames(set)[Biobase::fData(set)[ , '.type', drop=FALSE] == "numeric"]
            dta <- dta[ , sel, drop=FALSE]
            fdt <- Biobase::fData(set)[colnames(dta), ]

            if(sum(is.na(dta)) != 0 & !na.rm) {
                stop("Table ExposomeSet contains NA values.")
            } else if(sum(is.na(dta)) != 0 & na.rm) {
                if(verbose) {
                    message("Removing exposures with missing data.")
                }
                onc <- ncol(dta)
                dta <- dta[ , colSums(dta) == 0]
                if(verbose | warnings) {
                    r <- onc - ncol(dta)
                    warning("Removed ", r, " (", round(r/onc * 100, 2), "%) exposures from original ExpressionSet.")
                }
                rm(onc)

                fdt <- Biobase::fData(set)[colnames(dta), ]
            }

            dta_list[[ii]] <- dta
            fdt_list[[ii]] <- fdt

        } else if (is(set, "eSet")) {
            if(verbose) {
                message("Creating table for eSet-like objects")
            }
            dta <- t(Biobase::exprs(set))
            fdt <- Biobase::fData(set)[colnames(dta), ]

            if(sum(is.na(dta)) != 0 & !na.rm) {
                stop("Table ExpressionSet contains NA values.")
            } else if(sum(is.na(dta)) != 0 & na.rm) {
                if(verbose) {
                    message("Removing probes with missing data.")
                }
                onc <- ncol(dta)
                dta <- dta[ , colSums(dta) == 0]
                if(verbose | warnings) {
                    r <- onc - ncol(dta)
                    warning("Removed ", r, " (", round(r/onc * 100, 2), "%) probes from original ExpressionSet.")
                }
                rm(onc)

                fdt <- Biobase::fData(set)[colnames(dta), ]
            }

            dta_list[[ii]] <- dta
            fdt_list[[ii]] <- fdt
        } else if (is(set, "RangedSummarizedExperiment")) {
            if(verbose) {
                message("Creating table for RangedSummarizedExperiment")
            }
            dta <- t(SummarizedExperiment::assay(set))
            fdt <- as.data.frame(SummarizedExperiment::rowRanges(set)[colnames(dta), ])

            if(sum(is.na(dta)) != 0 & !na.rm) {
                stop("Table ExpressionSet contains NA values.")
            } else if(sum(is.na(dta)) != 0 & na.rm) {
                if(verbose) {
                    message("Removing probes with missing data.")
                }
                onc <- ncol(dta)
                dta <- dta[ , colSums(dta) == 0]
                if(verbose | warnings) {
                    r <- onc - ncol(dta)
                    warning("Removed ", r, " (", round(r/onc * 100, 2), "%) probes from original ExpressionSet.")
                }
                rm(onc)

                fdt <- Biobase::fData(set)[colnames(dta), ]
            }

            dta_list[[ii]] <- dta
            fdt_list[[ii]] <- fdt
        } else if (is(set, "SummarizedExperiment")) {
            if(verbose) {
                message("Creating table for SummarizedExperiment objects")
            }
            dta <- t(SummarizedExperiment::assay(set))
            fdt <- as.data.frame(SummarizedExperiment::rowData(set)[colnames(dta), ])

            if(sum(is.na(dta)) != 0 & !na.rm) {
                stop("Table ExpressionSet contains NA values.")
            } else if(sum(is.na(dta)) != 0 & na.rm) {
                if(verbose) {
                    message("Removing probes with missing data.")
                }
                onc <- ncol(dta)
                dta <- dta[ , colSums(dta) == 0]
                if(verbose | warnings) {
                    r <- onc - ncol(dta)
                    warning("Removed ", r, " (", round(r/onc * 100, 2), "%) probes from original ExpressionSet.")
                }
                rm(onc)

                fdt <- Biobase::fData(set)[colnames(dta), ]
            }

            dta_list[[ii]] <- dta
            fdt_list[[ii]] <- fdt
        }

        ii <- ii + 1
    }
    ## --------------------------------------------------------------------- ##
    names(dta_list) <- names(mds)
    names(fdt_list) <- names(mds)
    return(list(
        adata = dta_list,
        fdata = fdt_list
    ))
}