Functions to find different types of alternative splicing events from preprocessed GRanges exon data. Events include skipped exon (se), included exon (ie), mutatualy exclusive exons (mxe), retained intron (ri), and alternative 5' and 3' splice sites (a5ss / a3ss).
Usage
find_se(gr, type = c("boundary", "over", "in"), inverse = FALSE)
find_skipped_exons(gr, type = c("boundary", "over", "in"), inverse = FALSE)
find_ie(gr, type = c("boundary", "over", "in"))
find_included_exons(gr, type = c("boundary", "over", "in"))
find_mxe(gr, type = c("boundary", "in", "over"))
find_mutually_exclusive_exons(gr, type = c("boundary", "in", "over"))
find_ri(gr)
find_retained_introns(gr)
find_a5ss(gr)
find_alternative_5_prime_splice_sites(gr)
find_a3ss(gr)
find_alternative_3_prime_splice_sites(gr)
find_all_events(gr, type = c("boundary", "over", "in"), verbose = TRUE)Arguments
- gr
A GRanges object with exon annotations, including 'tx_id', 'exon', and 'coef_col' metadata columns and preprocessed with preprocess().
- type
The type of overlap to consider when identifying events.
- inverse
If TRUE, identifies included exons instead of skipped exons.
- verbose
If TRUE, prints progress messages. Default TRUE.
Value
A GRanges object with the detected exon ranges and the following additional metadata columns:
event_typeThe type of splicing event detected (e.g.
"se","ie","mxe","ri","a5ss","a3ss").event_tx_idTranscript ID of the paired transcript involved in the event.
event_estimateDTU coefficient of the paired transcript.
event_<col>One column per name in
metadata(gr)$additional_columns, prefixed withevent_, carrying the corresponding value from the paired transcript.
find_se(): skipped exons
find_ie(): included exons
find_mxe(): mutually exclusive exons
find_ri(): retained introns
find_a5ss(): alternative 5' splice sites
find_a3ss(): alternative 3' splice sites
find_all_events(): all detected events
Examples
# make some mock data and run the function
gr <- create_mock_data(n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4) |>
preprocess(coef_col = "estimate") |>
generate_se(n_events = 1)
# this should find the skipped exon events we generated
find_se(gr, type = "boundary")
#> GRanges object with 2 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr21 111-115 + | 2 5 3 -0.821465
#> [2] chr21 111-115 + | 2 7 3 -0.398338
#> event_type event_tx_id event_estimate
#> <character> <numeric> <numeric>
#> [1] se 8 0.272931
#> [2] se 8 0.272931
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
find_ie(gr, type = "boundary")
#> GRanges object with 0 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> -------
#> seqinfo: no sequences
# detect mutually exclusive exons
gr_mx <- create_mock_data(
n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4
) |>
preprocess(coef_col = "estimate") |>
generate_mxe(n_events = 1)
find_mxe(gr_mx, type = "boundary")
#> GRanges object with 2 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr22 11-15 + | 1 3 2 -0.591643
#> [2] chr22 21-25 + | 1 2 2 0.377796
#> event_type event_tx_id event_estimate
#> <character> <numeric> <numeric>
#> [1] mxe 2 0.377796
#> [2] mxe 3 -0.591643
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# detect retained introns
gr_ri <- create_mock_data(
n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4
) |>
preprocess(coef_col = "estimate") |>
generate_ri(n_events = 1)
find_ri(gr_ri)
#> GRanges object with 2 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr6 101-115 + | 2 6 2 0.409872
#> [2] chr6 101-115 + | 2 6 2 0.409872
#> event_type event_tx_id event_estimate
#> <character> <numeric> <numeric>
#> [1] ri 5 -0.162341
#> [2] ri 7 -0.573655
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# detect alternative 5' splice sites
gr_a5 <- create_mock_data(
n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4
) |>
preprocess(coef_col = "estimate") |>
generate_a5ss(n_events = 1)
find_a5ss(gr_a5)
#> GRanges object with 1 range and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr14 101-103 + | 2 7 2 0.992694
#> event_type event_tx_id event_estimate
#> <character> <numeric> <numeric>
#> [1] a5ss 5 -0.149921
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# detect alternative 3' splice sites
gr_a3 <- create_mock_data(
n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4
) |>
preprocess(coef_col = "estimate") |>
generate_a3ss(n_events = 1)
find_a3ss(gr_a3)
#> GRanges object with 1 range and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr9 109-115 + | 2 6 3 0.572669
#> event_type event_tx_id event_estimate
#> <character> <numeric> <numeric>
#> [1] a3ss 5 -0.765392
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# detect all event types at once
gr_all <- create_mock_data(
n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4
) |>
preprocess(coef_col = "estimate") |>
generate_se(n_events = 1)
find_all_events(gr_all, type = "boundary", verbose = FALSE)
#> GRanges object with 1 range and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr16 11-15 + | 1 1 2 -0.14205
#> event_type event_tx_id event_estimate
#> <character> <numeric> <numeric>
#> [1] se 4 0.990246
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths