Defines functions ideoView_qual

#' Check input to ideoView
#' Check that input to ideoView is properly formatted
#' @name ideoView_qual
#' @param x a data frame with rows representing cytogenetic bands for a genome.
#' The data frame should have columns "chrom", "chromStart", "chromEnd", "name",
#' "gieStain'.
#' @return data frame
#' @noRd

ideoView_qual <- function(x)
    # Check that input is a data frame
        memo <- paste0("Input does not appear to be a data frame... ",
                       "attempting to coerce.")
        x <- as.data.frame(x)
    # Check that proper columns are present
    col <- c("chrom", "chromStart", "chromEnd", "name", "gieStain")
    if(!all(col %in% colnames(x)))
        memo <- paste0("Did not detect correct columns in input to x, ",
                       "missing one of the following: ", toString(col))
    # check that the giestain column contains the proper levels
    gie_stain <- c('gneg',
                   paste0('gpos', 1:100))
    if(any(!x$gieStain %in% gie_stain))
        memo <- paste0("Found variable in column gieStain not recognized,",
                       " please ensure variable supplied are one of the",
                       " following: ", toString(gie_stain))

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GenVisR documentation built on Dec. 28, 2020, 2 a.m.