View source: R/analyze_switch_consequences.R
extractConsequenceEnrichmentComparison | R Documentation |
This function compares the enrichment of a consequences (f.x. domain gain) between two comparisons (ctrl vs ko1 compared to ctrl vs ko2) and reports whether there is a significant difference between the comparisons. It other words it compares the output of extractConsequenceEnrichment
.
extractConsequenceEnrichmentComparison(
switchAnalyzeRlist,
consequencesToAnalyze = 'all',
alpha=0.05,
dIFcutoff = 0.1,
countGenes = TRUE,
analysisOppositeConsequence=FALSE,
plot=TRUE,
localTheme = theme_bw(base_size = 14),
minEventsForPlotting = 10,
returnResult=TRUE
)
switchAnalyzeRlist |
A |
consequencesToAnalyze |
A string indicating which consequences should be considered. See details for description (note it is identical to the strings used with |
alpha |
The cutoff which the 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%). |
countGenes |
A logic indicating whether it is the number of genes (if TRUE) or isoform switches (if FALSE) which primary result in gain/loss that are counted. Default is TRUE. |
analysisOppositeConsequence |
A logic indicating whether reverse the analysis meaning if "Domain gains"" are analyze using default parameters setting |
plot |
A logic indicting whether the analysis should be plotted. If TRUE and |
localTheme |
General ggplo2 theme with which the plot is made, see |
minEventsForPlotting |
The minimum number of events (total gain/loss) must be present before the result is visualized. Default is 10. |
returnResult |
A logic indicating whether the analysis should be returned as a data.frame. If FALSE (and |
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 statistical summary for each opposing 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. Bioinformatics (2019).
analyzeSwitchConsequences
extractSwitchSummary
extractConsequenceEnrichment
extractConsequenceGenomeWide
### Load exampled data
data("exampleSwitchListAnalyzed")
extractConsequenceEnrichmentComparison( exampleSwitchListAnalyzed)
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