R/check_controlled_args.R

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

#' check_controlled_args
#' 
#' Check the input arguments of the 
#' \link[EWCE]{controlled_geneset_enrichment}.
#' 
#' @param hits Hit genes.
#' @param funcGenes \code{functional_genes} that are within
#'  \code{combinedGenes}.
#' @param combinedGenes \code{sct_data} genes that are in the background 
#' \code{bg}.
#' @inheritParams controlled_geneset_enrichment
#' @return Null output.
#' 
#' @keywords internal
check_controlled_args <- function(bg,
                                  sct_data,
                                  annotLevel,
                                  disease_genes,
                                  hits,
                                  functional_genes,
                                  funcGenes,
                                  combinedGenes) {
    err_msg <- paste0(
        "ERROR: no bg are present in the single cell",
        " dataset. Perhaps it is from the wrong species?"
    )
    if (sum(bg %in% rownames(sct_data[[annotLevel]]$mean_exp),
        na.rm = TRUE
    ) == 0) {
        stop(err_msg)
    }
    err_msg2 <- paste0(
        "ERROR: no disease_genes are present in the single cell",
        " dataset. Perhaps it is from the wrong species?"
    )
    if (sum(disease_genes %in% combinedGenes,
        na.rm = TRUE
    ) == 0) {
        stop(err_msg2)
    }
    err_msg3 <- paste0(
        "ERROR: insufficient disease_genes. Must provide at",
        " least five that are present in the background",
        " gene set & single cell dataset"
    )
    if (sum(hits %in% combinedGenes, na.rm = TRUE) < 5) {
        stop(err_msg3)
    }
    err_msg4 <- paste0(
        "ERROR: no functional_genes are present in the",
        " single cell dataset. Perhaps it is from the",
        " wrong species?"
    )
    if (sum(functional_genes %in% combinedGenes, na.rm = TRUE) == 0) {
        stop(err_msg4)
    }
    err_msg5 <- paste0(
        "ERROR: insufficient functional_genes Must provide",
        " at least five that are present in the background",
        " gene set & single cell dataset"
    )
    if (sum(funcGenes %in% combinedGenes, na.rm = TRUE) < 5) {
        stop(err_msg5)
    }
}