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Prepare exon ranges from a TxDb and DTU results table

Source: R/input_formatting.R
prepare_exons.Rd

Extracts exon ranges from a TxDb object, merges them with differential transcript usage (DTU) results, and returns a flat GRanges ready for preprocess.

Usage

prepare_exons(
  txdb,
  dtu_table,
  coef_col,
  tx_id_col = "tx_id",
  gene_id_col = "gene_id",
  verbose = TRUE
)

Arguments

txdb

A TxDb object (from GenomicFeatures).

dtu_table

A data.frame or tibble with DTU results. Must contain columns for transcript ID, gene ID, and a coefficient.

coef_col

Column name in dtu_table with the coefficient / effect size values.

tx_id_col

Column name in dtu_table with transcript IDs matching the TxDb transcript names. Default "tx_id".

gene_id_col

Column name in dtu_table with gene IDs. Default "gene_id".

verbose

Whether to print progress messages. Default TRUE.

Value

A GRanges object with metadata columns: gene_id, tx_id, exon_rank, the coefficient column, and any additional columns from dtu_table.

Examples


library(AnnotationHub)
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
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#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
library(AnnotationDbi)
#> Loading required package: stats4
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:AnnotationHub’:
#> 
#>     cache
#> Loading required package: IRanges
#> Loading required package: S4Vectors
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#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
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library(GenomicFeatures)
#> Loading required package: Seqinfo
#> Loading required package: GenomicRanges
library(tibble)

ah <- AnnotationHub()
txdb <- ah[["AH84134"]] # fly TxDb (Drosophila melanogaster)
#> loading from cache

# build a simulated DTU table from the TxDb transcripts
txps <- txdb |>
  AnnotationDbi::select(
    keys(txdb, "TXID"), c("TXNAME", "GENEID"), "TXID"
  ) |>
  tibble::as_tibble() |>
  dplyr::select(tx_id = TXNAME, gene_id = GENEID)|>
  dplyr::filter(!is.na(gene_id))
#> 'select()' returned 1:1 mapping between keys and columns

sim_dtu_table <- txps |>
  dplyr::mutate(
    padj = runif(dplyr::n()),
    effect_est = rnorm(dplyr::n())
  )

fly_exons <- prepare_exons(
  txdb, sim_dtu_table, coef_col = "effect_est", verbose = TRUE
)
#> Extracting exons from TxDb...
#> 'select()' returned 1:1 mapping between keys and columns
#> Mapping transcript IDs...
#> Merging DTU results onto exons...
#> Done. Returned 188169 exon ranges from 34920 unique transcripts.