R/in_crossomics_mcia.R

In isglobal-brge/omicRexposome: Exposome and omic data associatin and integration analysis

.crossomics_mcia <- function(object, ncomponents = 2, ...,
                             verbose = FALSE, warnings = TRUE) {

    ## --------------------------------------------------------------------- ##
    ## CREATE LIST OF TABLES IN BASE OF THE TYPE OF DATA
    dta_list <- in_mds_for_crosomics(object, na.rm = FALSE,
        verbose = verbose, warnings = warnings)

    fdt_list <- dta_list[["fdata"]]
    dta_list <- dta_list[["adata"]]

    dta_list <- lapply(dta_list, t)
    names(dta_list) <- names(fdt_list) <- names(object)
    ## --------------------------------------------------------------------- ##

    ## --------------------------------------------------------------------- ##
    ## PERFORM THE INTEGRATION WITH MCIA
    if(verbose) {
        message("Performing crossomics (MCIA)")
    }

    mres <- omicade4::mcia(dta_list, cia.nf = ncomponents)#, ...)
    ## --------------------------------------------------------------------- ##

    names(fdt_list) <- names(list)
    options = list(
        N = ncol(dta_list[[1]]),
        S = length(list),
        names = names(list),
        ncomponents = ncomponents,
        method = "mcia",
        package = "omicade4"
    )

    rs <- MultiDataSet::create_resultset(
        fOrigin = "crossomics",
        lResults = list("crossomics"=list("result" = mres, error=NA)),
        fData = fdt_list,
        lOptions = options
    )

    names(rs@fData) <- names(object)
    rs
}