extractSplicingEnrichment {IsoformSwitchAnalyzeR} | R Documentation |
This functions function analyzes for enrichment of specific consequnces by for each set of opposing consequnces (fx. exon skipping gain vs loss), by analyzing the fraction of events belonging to each type of consequence. It only summarizes the analysis perfromed with analyzeSwitchConsequences
extractSplicingEnrichment( switchAnalyzeRlist, splicingToAnalyze = 'all', alpha = 0.05, dIFcutoff = 0.1, onlySigIsoforms = FALSE, plot = TRUE, localTheme = theme_bw(base_size = 14), returnResult=FALSE, returnSummary=TRUE )
switchAnalyzeRlist |
A |
splicingToAnalyze |
A string indicating which consequnces should be considered. See details for description. Default is all. |
alpha |
The cutoff which the (callibrated) fdr correct p-values must be smaller than for calling significant switches. Default is 0.05. |
dIFcutoff |
The cutoff which the changes in (absolute) isoform usage must be larger than before an isoform is considered switching. This cutoff can remove cases where isoforms with (very) low dIF values are deemed significant and thereby included in the downstream analysis. This cutoff is analogous to having a cutoff on log2 fold change in a normal differential expression analysis of genes to ensure the genes have a certain effect size. Default is 0.1 (10%). |
onlySigIsoforms |
A logic indicating whether to only consider significant isoforms, meaning only analyzing genes where at least two isoforms which both have significant usage changes in opposite direction (quite strict) Naturally this only works if the isoform switch test used have isoform resolution (which the build in isoformSwitchTestDEXSeq has). If FALSE all isoforms with an absolute dIF value larger than |
plot |
A logic indicting whether the analysis should be plotted. Default is TRUE. |
localTheme |
General ggplo2 theme with which the plot is made, see |
returnResult |
A logic indicating whether the analysis should be returned as a data.frame. Default is FALSE. |
returnSummary |
A logic indicating whether to return the statistical summary (if TRUE) or the underlying data (if FALSE). Default is TRUE. |
The classification of alternative splicing is always compared to the hypothetical pre-mRNA constructed by concatenating all exons from isoforms of the same gene.
The alternative splicing types, which can be passed to splicingToAnalyze
must be a combination of:
all
: All of the alternative splicing types indicated below.
IR
: Intron Retention.
A5
: Alternative 5' donor site (changes in the 5'end of the upstream exon).
A3
: Alternative 3' acceptor site (changes in the 3'end of the downstream exon).
ATSS
: Alternative Transcription Start Site.
ATTS
: Alternative Transcription Termination Site.
ES
: Exon Skipping.
MES
: Multiple Exon Skipping. Skipping of >1 consequtive exons.
MEE
: Mutually Exclusive Exons.
For details of how to interpret the splice events see the details
section of analyzeAlternativeSplicing
.
The significance test is performed with R's build in prop.test()
with default parameters and resulting p-values are corrected via p.adjust() using FDR (Benjamini-Hochberg).
If returnResult=TRUE
a data.frame with the statisitcal summary for each oposing consequences in each comparison. If plot=TRUE
a plot summarizing the proportions is also created of switches with specific consequences is created.
Kristoffer Vitting-Seerup
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
Vitting-Seerup et al. IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences. bioRxiv (2018).
isoformSwitchTestDEXSeq
isoformSwitchTestDRIMSeq
analyzeAlternativeSplicing
extractSplicingSummary
extractSplicingEnrichmentComparison
extractSplicingGenomeWide
### Load example data data("exampleSwitchListAnalyzed") extractSplicingEnrichment( exampleSwitchListAnalyzed )