inst/shiny/expt_app_helpers.R

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

get_annots <- function(annots = "TMRC2", orgdb = "org.Lpanamensis.MHOMCOL81L13.v46.eg.db") {
  loaded <- do.call("library", list(orgdb))
  annotations <- NULL
  if (annots == "TMRC2") {
    pan_db <- get0(orgdb)
    all_fields <- AnnotationDbi::columns(pan_db)

    all_lp_annot <- sm(load_orgdb_annotations(
        pan_db, keytype = "gid",
        fields = c("annot_gene_entrez_id", "annot_gene_name",
                   "annot_strand", "annot_chromosome", "annot_cds_length",
                   "annot_gene_product")))[["genes"]]

    lp_go <- sm(load_orgdb_go(pan_db))
    lp_lengths <- all_lp_annot[, c("gid", "annot_cds_length")]
    colnames(lp_lengths)  <- c("ID", "length")
    all_lp_annot[["annot_gene_product"]] <- tolower(all_lp_annot[["annot_gene_product"]])
    orthos <- sm(EuPathDB::extract_eupath_orthologs(db = pan_db))
    annotations <- all_lp_annot
  } else if (annots == "TMRC3") {
    hs_annot <- sm(load_biomart_annotations(year="2020"))
    hs_annot <- hs_annot[["annotation"]]
    hs_annot[["transcript"]] <- paste0(rownames(hs_annot), ".", hs_annot[["version"]])
    rownames(hs_annot) <- make.names(hs_annot[["ensembl_gene_id"]], unique=TRUE)
    tx_gene_map <- hs_annot[, c("transcript", "ensembl_gene_id")]
    annotations <- hs_annot
  }
  return(annotations)

}

get_data <- function(datadir) {
  expt <- NULL
  #if (data == "TMRC2") {
   # if (file.exists("/mnt/cbcb/fs00_reesyxan/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/rda/expt.rda")) {
    #  load("/mnt/cbcb/fs00_reesyxan/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/rda/expt.rda")
     # expt <- expt %>%
      #  set_expt_conditions(fact = "zymodemecategorical") %>%
       # subset_expt(nonzero = 8550) %>%
        #subset_expt(coverage = 5000000) %>%
        #semantic_expt_filter(semantic = c("amastin", "gp63", "leishmanolysin"),
         #                    semantic_column = "annot_gene_product")
    #}

  #} else if (data == "TMRC3") {
   # if (file.exists("/mnt/cbcb/fs00_reesyxan/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/rda/hs_expt_all-v202110.rda")) {
    #  load("/mnt/cbcb/fs00_reesyxan/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/rda/hs_expt_all-v202110.rda")
     # expt <- expt %>%
      #  exclude_genes_expt(column="gene_biotype", method="keep",
       #                    patterns="protein_coding", meta_column="ncrna_lost")
  #  }
  #}
  if (file.exists(datadir)){
    #"/mnt/cbcb/fs00_reesyxan/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/rda/expt.rda")) {
    load(datadir)
  }
  
  return(expt)
}

substrRight <- function(x, n) {
  substr(x, nchar(x) - n + 1, nchar(x))
}