kvittingseerup
extractSwitchOverlap does not recognize switch analysis
I wanted to generate venn diagrams from the vignette on the following list:
asl2
This switchAnalyzeRlist list contains: 1612 isoforms from 301 genes 6 comparison from 4 conditions (in total 8 samples) Switching features: Comparison Isoforms Switches Genes 1 DHX29 vs MPP8 108 117 76 2 DHX29 vs TASOR 87 104 68 3 DHX29 vs WT 187 219 130 4 MPP8 vs TASOR 133 151 93 5 MPP8 vs WT 219 239 149 6 TASOR vs WT 137 165 99 7 Combined 529 730 301
Feature analyzed: [1] "Isoform Switch Identification, ORFs, ntSequence, aaSequence, Alternative splicing"
extractSwitchOverlap produces an error
extractSwitchOverlap( asl2, filterForConsequences=TRUE, plotIsoforms = FALSE )
Error in extractSwitchOverlap(asl2, filterForConsequences = TRUE, plotIsoforms = FALSE) : The switchAnalyzeRlist does not contain isoform switching analysis. Please run the 'isoformSwitchTestDEXSeq' or 'isoformSwitchTestDRIMSeq' function first.
So I do what it asks
asl3<-isoformSwitchTestDEXSeq(asl2)
Step 1 of 2: Testing each pairwise comparisons with DEXSeq (this might be a bit slow)... Estimated time (for dataset with ~30.000 isoforms): 6.6 min |================================================================================================================================| 100% Step 2 of 2: Integrating result into switchAnalyzeRlist... Isoform switch analysis was performed for 1728 gene comparisons (100%). Total runtime: 3.72 min Done
The same error is produced with the new list.
extractSwitchOverlap( asl3, filterForConsequences=TRUE, plotIsoforms = FALSE )
Error in extractSwitchOverlap(asl3, filterForConsequences = TRUE, plotIsoforms = FALSE) : The switchAnalyzeRlist does not contain isoform switching analysis. Please run the 'isoformSwitchTestDEXSeq' or 'isoformSwitchTestDRIMSeq' function first.
Which version of IsoformSwitchAnalyzeR are you using?
Also you might run into a problem with 6 comparisons. That cannot fit in a wenn diagram.
