create_te_count_table.R

# reads in a folder with TE counts from the Hammel TETranscripts tools
create_te_count_table = function(feature_count_folder, suffix = ".Aligned.sorted.out.bam",prefix = ""){
    library(data.table)
    # feature counts gives you feature coutns and summariues, given a folder name get a list of files that don't contain
    # the word summary
    feature_count_files = grep(list.files(path=feature_count_folder,full.names = TRUE), pattern='summary', inv=T, value=T)
    # from the list, read them all
    l <- lapply(feature_count_files, fread)
    # make it into a data table
    wide_feature_counts = setDT(unlist(l, recursive = FALSE), check.names = TRUE)[]

    # there's only a few columns we really want from this table it's going to be
    # Geneid and the things that labeled by their file name so we do two things
    # first when we do this setDT unlist thing names become X.path.to. so we'lre gooing to take the feature counts files and replace the / with .
    selector_list = c("gene.TE",names(wide_feature_counts)[grepl("^X",names(wide_feature_counts))])
    # take only those columns
    wide_feature_counts = wide_feature_counts[,.SD, .SDcols = selector_list]
    # ----remove unnecessary information from the column names
    if(suffix != ""){
        colnames(wide_feature_counts) = gsub(suffix,"",colnames(wide_feature_counts))
    }
    if(prefix != ""){
        colnames(wide_feature_counts) = gsub(prefix,"",colnames(wide_feature_counts))
    }
    return(wide_feature_counts)
}