Prepare exons from two transcript partitions — prepare_exons_by

Combines two transcript partitions (up- and down-regulated) and assigns an estimate coefficient: +1 to up and -1 to down. Accepts either GRanges objects or character vectors of transcript IDs (in which case txdb is required to look up exon coordinates). The result is ready to pass to preprocess with coef_col = "estimate".

Usage

prepare_exons_by_partition(
  up,
  down,
  txdb = NULL,
  tx_id_col = "TXNAME",
  verbose = TRUE
)

Arguments

up: A GRanges object or character vector of transcript IDs for the upregulated partition (assigned estimate = +1).
down: A GRanges object or character vector of transcript IDs for the downregulated partition (assigned estimate = -1).
txdb: A TxDb object (from GenomicFeatures). Required when up and down are character vectors of transcript IDs.
tx_id_col: The keytype in txdb matching the transcript IDs in up and down. Default "TXNAME". Only used when up and down are character vectors. See AnnotationDbi::keytypes(txdb) for available options.
verbose: Whether to print progress messages. Default TRUE.

Value

A combined GRanges object with an estimate column (+1 for up, -1 for down), ready for preprocess.

Details

When up and down are GRanges, both must have exon_rank, gene_id, and tx_id metadata columns. Extra columns are kept; if one object lacks a column present in the other, those entries receive NA.

Examples


# GRanges input
gr <- create_mock_data(n_genes = 1, n_tx_per_gene = 4, n_exons_per_tx = 4)
gr <- generate_se(gr, n_events = 1)
gr_down <- gr[gr$estimate < 0]
gr_up <- gr[gr$estimate > 0]
prepare_exons_by_partition(gr_up, gr_down) |>
  preprocess(coef_col = "estimate")
#> GRanges object with 15 ranges and 7 metadata columns:
#>        seqnames    ranges strand |   gene_id     tx_id exon_rank  estimate
#>           <Rle> <IRanges>  <Rle> | <integer> <numeric> <integer> <integer>
#>    [1]    chr11       1-5      + |         1         2         1         1
#>    [2]    chr11     21-25      + |         1         2         2         1
#>    [3]    chr11     31-35      + |         1         2         3         1
#>    [4]    chr11       1-5      + |         1         4         1         1
#>    [5]    chr11     11-15      + |         1         4         2         1
#>    ...      ...       ...    ... .       ...       ...       ...       ...
#>   [11]    chr11     31-35      + |         1         1         4        -1
#>   [12]    chr11       1-5      + |         1         3         1        -1
#>   [13]    chr11     11-15      + |         1         3         2        -1
#>   [14]    chr11     21-25      + |         1         3         3        -1
#>   [15]    chr11     31-35      + |         1         3         4        -1
#>                key    nexons  internal
#>        <character> <integer> <logical>
#>    [1]         2-1         3     FALSE
#>    [2]         2-2         3      TRUE
#>    [3]         2-3         3     FALSE
#>    [4]         4-1         4     FALSE
#>    [5]         4-2         4      TRUE
#>    ...         ...       ...       ...
#>   [11]         1-4         4     FALSE
#>   [12]         3-1         4     FALSE
#>   [13]         3-2         4      TRUE
#>   [14]         3-3         4      TRUE
#>   [15]         3-4         4     FALSE
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths