Functions to introduce specific types of alternative splicing events into mock GRanges data for testing purposes.
Usage
generate_se(gr, n_events = 1)
generate_mxe(gr, n_events = 1)
generate_ri(gr, n_events = 1)
generate_a5ss(gr, n_events = 1)
generate_a3ss(gr, n_events = 1)Value
generate_se(): A GRanges object with skipped exon
events introduced
generate_mxe(): A GRanges object with mutually exclusive exon
events introduced
generate_ri(): A GRanges object with retained intron
events introduced
generate_a5ss(): A GRanges object with alternative 5' splice site
events introduced
generate_a3ss(): A GRanges object with alternative 3' splice site
events introduced
Examples
gr <- create_mock_data(
n_genes = 2, n_tx = 4, n_exons = 4
)
generate_se(gr, n_events = 1)
#> GRanges object with 31 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr10 1-5 + | 1 1 1 -0.103009
#> [2] chr10 11-15 + | 1 1 2 -0.103009
#> [3] chr10 21-25 + | 1 1 3 -0.103009
#> [4] chr10 31-35 + | 1 1 4 -0.103009
#> [5] chr10 1-5 + | 1 2 1 0.855840
#> ... ... ... ... . ... ... ... ...
#> [27] chr10 131-135 + | 2 7 4 0.656029
#> [28] chr10 101-105 + | 2 8 1 -0.798687
#> [29] chr10 111-115 + | 2 8 2 -0.798687
#> [30] chr10 121-125 + | 2 8 3 -0.798687
#> [31] chr10 131-135 + | 2 8 4 -0.798687
#> key nexons internal
#> <character> <integer> <logical>
#> [1] 1-1 4 FALSE
#> [2] 1-2 4 TRUE
#> [3] 1-3 4 TRUE
#> [4] 1-4 4 FALSE
#> [5] 2-1 3 FALSE
#> ... ... ... ...
#> [27] 7-4 4 FALSE
#> [28] 8-1 4 FALSE
#> [29] 8-2 4 TRUE
#> [30] 8-3 4 TRUE
#> [31] 8-4 4 FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
gr <- create_mock_data(
n_genes = 2, n_tx = 4, n_exons = 4
)
generate_mxe(gr, n_events = 1)
#> GRanges object with 30 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr9 1-5 + | 1 1 1 -0.404016
#> [2] chr9 11-15 + | 1 1 2 -0.404016
#> [3] chr9 21-25 + | 1 1 3 -0.404016
#> [4] chr9 31-35 + | 1 1 4 -0.404016
#> [5] chr9 1-5 + | 1 2 1 0.395668
#> ... ... ... ... . ... ... ... ...
#> [26] chr9 111-115 + | 2 7 2 -0.838310
#> [27] chr9 131-135 + | 2 7 3 -0.838310
#> [28] chr9 101-105 + | 2 8 1 0.311965
#> [29] chr9 121-125 + | 2 8 2 0.311965
#> [30] chr9 131-135 + | 2 8 3 0.311965
#> key nexons internal
#> <character> <integer> <logical>
#> [1] 1-1 4 FALSE
#> [2] 1-2 4 TRUE
#> [3] 1-3 4 TRUE
#> [4] 1-4 4 FALSE
#> [5] 2-1 4 FALSE
#> ... ... ... ...
#> [26] 7-2 3 TRUE
#> [27] 7-3 3 FALSE
#> [28] 8-1 3 FALSE
#> [29] 8-2 3 TRUE
#> [30] 8-3 3 FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
gr <- create_mock_data(
n_genes = 2, n_tx = 4, n_exons = 4
)
generate_ri(gr, n_events = 1)
#> GRanges object with 31 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr8 1-5 + | 1 1 1 -0.586908
#> [2] chr8 11-15 + | 1 1 2 -0.586908
#> [3] chr8 21-25 + | 1 1 3 -0.586908
#> [4] chr8 31-35 + | 1 1 4 -0.586908
#> [5] chr8 1-5 + | 1 2 1 0.134598
#> ... ... ... ... . ... ... ... ...
#> [27] chr8 121-125 + | 2 8 3 0.0177871
#> [28] chr8 131-135 + | 2 8 4 0.0177871
#> [29] chr8 1-5 + | 1 4 1 0.3303049
#> [30] chr8 11-25 + | 1 4 2 0.3303049
#> [31] chr8 31-35 + | 1 4 3 0.3303049
#> key nexons internal
#> <character> <integer> <logical>
#> [1] 1-1 4 FALSE
#> [2] 1-2 4 TRUE
#> [3] 1-3 4 TRUE
#> [4] 1-4 4 FALSE
#> [5] 2-1 4 FALSE
#> ... ... ... ...
#> [27] 8-3 4 TRUE
#> [28] 8-4 4 FALSE
#> [29] 4-1 3 FALSE
#> [30] 4-2 3 TRUE
#> [31] 4-3 3 FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
gr <- create_mock_data(
n_genes = 2, n_tx = 4, n_exons = 4
)
generate_a5ss(gr, n_events = 1)
#> GRanges object with 32 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr20 1-5 + | 1 1 1 -0.478438
#> [2] chr20 11-15 + | 1 1 2 -0.478438
#> [3] chr20 21-25 + | 1 1 3 -0.478438
#> [4] chr20 31-35 + | 1 1 4 -0.478438
#> [5] chr20 1-5 + | 1 2 1 0.886854
#> ... ... ... ... . ... ... ... ...
#> [28] chr20 131-135 + | 2 7 4 0.629192
#> [29] chr20 101-105 + | 2 8 1 -0.858070
#> [30] chr20 111-115 + | 2 8 2 -0.858070
#> [31] chr20 121-125 + | 2 8 3 -0.858070
#> [32] chr20 131-135 + | 2 8 4 -0.858070
#> key nexons internal
#> <character> <integer> <logical>
#> [1] 1-1 4 FALSE
#> [2] 1-2 4 TRUE
#> [3] 1-3 4 TRUE
#> [4] 1-4 4 FALSE
#> [5] 2-1 4 FALSE
#> ... ... ... ...
#> [28] 7-4 4 FALSE
#> [29] 8-1 4 FALSE
#> [30] 8-2 4 TRUE
#> [31] 8-3 4 TRUE
#> [32] 8-4 4 FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
gr <- create_mock_data(
n_genes = 2, n_tx = 4, n_exons = 4
)
generate_a3ss(gr, n_events = 1)
#> GRanges object with 32 ranges and 7 metadata columns:
#> seqnames ranges strand | gene_id tx_id exon_rank estimate
#> <Rle> <IRanges> <Rle> | <integer> <numeric> <integer> <numeric>
#> [1] chr14 1-5 + | 1 1 1 -0.741426
#> [2] chr14 11-15 + | 1 1 2 -0.741426
#> [3] chr14 21-25 + | 1 1 3 -0.741426
#> [4] chr14 31-35 + | 1 1 4 -0.741426
#> [5] chr14 1-5 + | 1 2 1 0.367170
#> ... ... ... ... . ... ... ... ...
#> [28] chr14 131-135 + | 2 7 4 0.655003
#> [29] chr14 101-105 + | 2 8 1 -0.744885
#> [30] chr14 111-115 + | 2 8 2 -0.744885
#> [31] chr14 121-125 + | 2 8 3 -0.744885
#> [32] chr14 131-135 + | 2 8 4 -0.744885
#> key nexons internal
#> <character> <integer> <logical>
#> [1] 1-1 4 FALSE
#> [2] 1-2 4 TRUE
#> [3] 1-3 4 TRUE
#> [4] 1-4 4 FALSE
#> [5] 2-1 4 FALSE
#> ... ... ... ...
#> [28] 7-4 4 FALSE
#> [29] 8-1 4 FALSE
#> [30] 8-2 4 TRUE
#> [31] 8-3 4 TRUE
#> [32] 8-4 4 FALSE
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths