R/check_controlledCTs.R

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

#' Check controlled cell type names
#' 
#' Check the cell types in 'controlledCT' exist
#' at the relevant annotation level.
#' 
#' @inheritParams calculate_conditional_geneset_enrichment
#' 
#' @return Null output.
#' 
#' @keywords internal
check_controlledCTs <- function(ctd,
                                controlledCTs,
                                controlledAnnotLevel){
    for (i in seq_len(length(controlledCTs))) {
        annotLvlCTs <- colnames(ctd[[
            as.numeric(controlledAnnotLevel)]]$specificity)
        reqCT <- controlledCTs[[i]]
        if (!reqCT %in% annotLvlCTs) {
            stopper("Cell type specified by controlledAnnotLevel",
                    "cannot be found in ctd level",controlledAnnotLevel,":",
                    reqCT) 
        }
    }
}