R/dict.r

In BioHPC/LONGO: Long gene expression as a metric for neuronal identity

#' LONGO dictionary function
#'
#' This is a internal function. This function creates and returns a dictionary
#' based on the user inputted values. Used to quickly link expression data
#' with names and lengths.
#'
#' @param data.df inputed data
#' @param biomaRt.df biomaRt database
#' @importFrom hash keys
#' @importFrom hash .set
#' @return returns a dictionary
dict <- function(data.df, biomaRt.df) {
    symbol.dict <- hash::hash(keys = data.df[, 1], values = NA)
    hash::.set(symbol.dict, keys = biomaRt.df[, 1], values=biomaRt.df[, 2])
    len.dict <- hash::hash(keys = data.df[, 1], values=NA)
    hash::.set(len.dict, keys = biomaRt.df[, 1], values=biomaRt.df[, 3])

    symdict.fun <- function(key) {
        return(symbol.dict[[key]])
    }
    lendict.fun <- function(key) {
        return(len.dict[[key]])
    }
    #get lengths and names
    data.df$symbol <- apply(as.matrix(data.df[, 1]), 1, symdict.fun)
    data.df$length <- apply(as.matrix(data.df[, 1]), 1, lendict.fun)
    #remove na's
    data.df <-data.df[!(is.na(data.df[, (ncol(data.df) - 1)]) |
        (data.df[, (ncol(data.df) - 1)] == "")), ]
    data.df <-data.df[!(is.na(data.df[, (ncol(data.df))]) |
        (data.df[, (ncol(data.df))] == "")), ]
return(data.df)
}