A dataset of skipped exon (SE) alternative splicing events generated by rMATS, provided for testing and demonstration of the splicing map and sequence motif analysis functions in RNAPeaks.
Format
A data frame with 87,736 observations and 23 variables:
- ID
Event ID
- GeneID
Ensembl gene ID
- geneSymbol
Gene symbol
- chr
Chromosome
- strand
Strand (+ or -)
- exonStart_0base
Skipped exon start position (0-based)
- exonEnd
Skipped exon end position
- upstreamES
Upstream exon start position
- upstreamEE
Upstream exon end position
- downstreamES
Downstream exon start position
- downstreamEE
Downstream exon end position
- ID.1
Duplicate ID column
- IJC_SAMPLE_1
Inclusion junction counts for sample 1
- SJC_SAMPLE_1
Skipping junction counts for sample 1
- IJC_SAMPLE_2
Inclusion junction counts for sample 2
- SJC_SAMPLE_2
Skipping junction counts for sample 2
- IncFormLen
Inclusion form length
- SkipFormLen
Skipping form length
- PValue
P-value for differential splicing
- FDR
False discovery rate adjusted p-value
- IncLevel1
Inclusion levels for sample 1
- IncLevel2
Inclusion levels for sample 2
- IncLevelDifference
Difference in inclusion levels between samples (positive = more inclusion in sample 1; negative = more skipping)
Source
Generated with rMATS (https://rnaseq-mats.sourceforge.net/) from K562 eCLIP data.
Examples
data(sample_se.mats)
head(sample_se.mats)
#> ID GeneID geneSymbol chr strand exonStart_0base exonEnd
#> 1 0 ENSG00000281903 LINC02246 chr21 - 14853273 14853431
#> 2 1 ENSG00000281903 LINC02246 chr21 - 14853273 14853431
#> 3 2 ENSG00000281903 LINC02246 chr21 - 14857541 14857708
#> 4 3 ENSG00000235609 <NA> chr21 - 14857541 14857708
#> 5 14 ENSG00000291050 TEKT4P2 chr21 - 9069153 9069341
#> 6 15 ENSG00000291050 TEKT4P2 chr21 - 9069444 9069599
#> upstreamES upstreamEE downstreamES downstreamEE ID.1 IJC_SAMPLE_1
#> 1 14825522 14825624 14857541 14857708 0 17,10,13
#> 2 14837181 14837823 14857541 14857708 1 13,8,20
#> 3 14825522 14825624 14902898 14903015 2 13,6,13
#> 4 14825522 14825624 15014343 15014430 3 14,10,15
#> 5 9068358 9068659 9069444 9069599 14 2,0,0
#> 6 9068324 9068659 9070213 9070436 15 23,21,42
#> SJC_SAMPLE_1 IJC_SAMPLE_2 SJC_SAMPLE_2 IncFormLen SkipFormLen PValue
#> 1 13,4,13 34,22,21 22,26,29 300 150 0.4074983162
#> 2 0,0,2 32,13,9 6,4,1 300 150 0.0003374221
#> 3 0,0,0 22,26,29 1,0,0 300 150 1.0000000000
#> 4 0,2,0 32,38,37 0,0,2 300 150 1.0000000000
#> 5 12,11,16 0,0,0 4,5,10 300 150 1.0000000000
#> 6 15,13,6 7,13,19 3,5,6 300 150 0.8530224703
#> FDR IncLevel1 IncLevel2 IncLevelDifference
#> 1 1.00000000 0.395,0.556,0.333 0.436,0.297,0.266 0.095
#> 2 0.01258623 1.0,1.0,0.833 0.727,0.619,0.818 0.223
#> 3 1.00000000 1.0,1.0,1.0 0.917,1.0,1.0 0.028
#> 4 1.00000000 1.0,0.714,1.0 1.0,1.0,0.902 -0.063
#> 5 1.00000000 0.077,0.0,0.0 0.0,0.0,0.0 0.026
#> 6 1.00000000 0.434,0.447,0.778 0.538,0.565,0.613 -0.019
if (FALSE) { # \dontrun{
createSplicingMap(bed_file = sample_bed, SEMATS = sample_se.mats)
createSequenceMap(SEMATS = sample_se.mats, sequence = "CCCC")
} # }