R/columnsAsCharacter.R

In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

# Change all factor columns of tSet data.frames to character
#
#
# @importFrom maggitr %<>%
# @importFrom dplyr mutate_if
columnsAsCharacter <- function(tSet) {
    for (mDataType in names(molecularProfilesSlot(tSet))) {
        phenoInfo(tSet, mDataType) %<>%
            tibble::rownames_to_column() %>%
            dplyr::mutate_if(is.factor, as.character) %>%
            tibble::column_to_rownames()

        featureInfo(tSet, mDataType) %<>%
            tibble::rownames_to_column() %>%
            dplyr::mutate_if(is.factor, as.character) %>%
            tibble::column_to_rownames()
    }
    if (length(sensitivityInfo(tSet)) > 0) {
        sensitivityInfo(tSet) %<>%
            tibble::rownames_to_column() %>%
            dplyr::mutate_if(is.factor, as.character) %>%
            tibble::column_to_rownames()
    }
    sampleInfo(tSet) %<>%
        tibble::rownames_to_column() %>%
        dplyr::mutate_if(is.factor, as.character) %>%
        tibble::column_to_rownames()

    treatmentInfo(tSet) %<>%
        tibble::rownames_to_column() %>%
        dplyr::mutate_if(is.factor, as.character) %>%
        tibble::column_to_rownames()

    return(tSet)
}

## TODO:: Determine how to use list.filter to recursively return all data.frames in a nested lsit
## TODO:: Write a recursive functions to return all non-list elements in a nested list