truncateTxsPolyA: Truncate transcripts at polyA sites
In TAPseq: Targeted scRNA-seq primer design for TAP-seq

Description Usage Arguments Value Methods (by class) Examples

Truncate transcripts at overlapping polyadenylation (polyA) sites to infer likely 3' ends of transcripts. This is crucial to correctly design TAP-seq primers that amplify fragments of specific lengths. Typically the exons of all annotated transcripts per target gene are provided as input. If a polyA site overlaps a single transcript of a given gene, this transcript is truncated and returned. In case a polyA site overlaps multiple transcripts of the same gene, a "metatranscript" consisting of all annotated exons of the overlapping transcripts is generated and truncated. No statements about expressed transcripts can be made if no overlapping polyA sites are found for any transcripts of a gene. In that case a "meta transcript" consisting of the merged exons of that gene is generated and returned.

truncateTxsPolyA(
  transcripts,
  polyA_sites,
  extend_3prime_end = 0,
  polyA_select = c("downstream", "upstream", "score"),
  transcript_id = "transcript_id",
  gene_id = "gene_id",
  exon_number = "exon_number",
  ignore_strand = FALSE,
  parallel = FALSE
)

## S4 method for signature 'GRanges'
truncateTxsPolyA(
  transcripts,
  polyA_sites,
  extend_3prime_end = 0,
  polyA_select = c("downstream", "upstream", "score"),
  transcript_id = "transcript_id",
  gene_id = "gene_id",
  exon_number = "exon_number",
  ignore_strand = FALSE,
  parallel = FALSE
)

## S4 method for signature 'GRangesList'
truncateTxsPolyA(
  transcripts,
  polyA_sites,
  extend_3prime_end = 0,
  polyA_select = c("downstream", "upstream", "score"),
  transcript_id = "transcript_id",
  gene_id = "gene_id",
  exon_number = "exon_number",
  ignore_strand = FALSE,
  parallel = FALSE
)

`transcripts`	A `GRanges` or `GRangesList` object containing exons of the transcripts to be truncated. Transcripts for multiple genes can be provided as `GRanges` objects within a `GRangesList`.
`polyA_sites`	A `GRanges` object containing the polyA sites. This needs to contain a metadata entry names "score" if the option `polyA_select = "score"` is used. PolyA sites can be either obtained via running `inferPolyASites` or imported from an existing .bed file via `import`.
`extend_3prime_end`	Specifies how far (bp) 3' ends of transcripts should be extended when looking for overlapping polyA sites (default = 0). This enables capturing of polyA sites that occur downstream of annotated 3' ends.
`polyA_select`	Specifies which eurisic should be used to select the polyA site used to truncate the transcripts if multiple overlapping polyA sites are found. By default `"downstream"` is used which choses the most downstream polyA site. `"score"` selects the polyA site with the highest score, which correspons to the read coverage when using `inferPolyASites` to estimate polyA sites.
`transcript_id`	(character) Name of the column in the metadata of `transcripts` providing transcript id for each exon (default: `"transcript_id"`). Set to `NULL` to ignore transcript ids and assume that all exons per gene belong to the same transcript.
`gene_id, exon_number`	(character) Optional names of columns in metadata of `transcripts` containing gene id and exon number. These are only used to create new metadata when merging multiple transcripts into a meta transcript.
`ignore_strand`	(logical) Specifies whether the strand of polyA sites should be ignored when looking for overlapping polyA sites. Default is `FALSE` and therefore only polyA sites on the same strand as the transcripts are considered. PolyA sites with strand `*` has the same effect as `ignore_strand = TRUE`.
`parallel`	(logical) Triggers parallel computing using the `BiocParallel` package. This requires that a parallel back-end was registered prior to executing the function. (default: `FALSE`).

Either a GRanges or GRangesList object containing the truncated transcripts.

GRanges: Truncate transcripts of one gene provided as GRanges object
GRangesList: Truncate transcripts of multiple genes provided as GRangesList

library(GenomicRanges)

# protein-coding exons of genes within chr11 region
data("chr11_genes")
target_genes <- split(chr11_genes, f = chr11_genes$gene_name)

# only retain first 2 target genes, because truncating transcripts is currently computationally
# quite costly. try using BiocParallel for parallelization (see ?truncateTxsPolyA).
target_genes <- target_genes[1:2]

# example polyA sites for these genes
data("chr11_polyA_sites")

# truncate target genes at most downstream polyA site (default)
truncated_txs <- truncateTxsPolyA(target_genes, polyA_sites = chr11_polyA_sites)

# change polyA selection to "score" (read coverage of polyA sites) and extend 3' end of target
# genes by 50 bp (see ?truncateTxsPolyA).
truncated_txs <- truncateTxsPolyA(target_genes, polyA_sites = chr11_polyA_sites,
                                  polyA_select = "score", extend_3prime_end = 50)