extractConsequenceSummary: Analyze Switch Consequences

In kvittingseerup/IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Analyze Switch Consequences

Description

This functions function summarizes the individual types of consequences for each gene or the pairwise switches and plots and/or returns a data.frame with the information

Usage

extractConsequenceSummary(
    switchAnalyzeRlist,
    consequencesToAnalyze='all',
    includeCombined=FALSE,
    asFractionTotal=FALSE,
    alpha=0.05,
    dIFcutoff=0.1,
    plot=TRUE,
    plotGenes=FALSE,
    simplifyLocation = TRUE,
    removeEmptyConsequences = FALSE,
    localTheme=theme_bw(),
    returnResult=FALSE
)

Arguments

switchAnalyzeRlist	A switchAnalyzeRlist object where analyzeSwitchConsequences() have been run to identify consequences of isoform switches
consequencesToAnalyze	A string indicating which consequences should be considered. See detail section of analyzeSwitchConsequences for description . Default is all consequences analyzed with analyzeSwitchConsequences.
includeCombined	A logic indicating whether an analysis of how many (how large a fraction) of genes have any type of functional consequence.
asFractionTotal	A logic indicating whether the consequences should be summarized calculated as numbers (if FALSE) or as a fraction of the total number of switches/genes (as indicated by plotGenes). Default is FALSE.
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%).
plot	A logic indicting whether the analysis should be plotted. If TRUE and returnResult = FALSE the ggplot2 object will be returned instead. Default is TRUE.
plotGenes	A logic indicating whether to plot the number/fraction of genes with (if TRUE) or isoforms (if FALSE) involved with isoform switches with functional consequences (both filtered via alpha and dIFcutoff.
simplifyLocation	A logic indicating whether to simplify the switches involved in changes in sub-cellular localizations (due the the hundreds of possible combinations). Done by only considering where the isoform used more has a location switch to. Default is TRUE.
removeEmptyConsequences	A logic indicating whether to remove consequenses analyzed but where no differences was found (those showing zero in the plot). Default is FALSE.
localTheme	General ggplo2 theme with which the plot is made, see ?ggplot2::theme for more info. Default is theme_bw().
returnResult	A logic indicating whether the summarized results should be returned as a data.frame. If FALSE (and plot=TRUE) the ggplot2 object will be returned instead. Default is FALSE.

Details

A less detailed version just summarizing the number of switches with functional consequences can be obtained by setting filterForConsequences=TRUE in the extractSwitchSummary function.

For details on the arguments passed to consequencesToAnalyze please see details section of analyzeSwitchConsequences.

Value

If returnResult=TRUE a data.frame with the number (and fraction) of switches with specific consequences in each condition is returned. If plot=TRUE a plot summarizing the number (or fraction) of switches with specific consequences is created.

Author(s)

Kristoffer Vitting-Seerup

References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

See Also

analyzeSwitchConsequences
extractConsequenceEnrichment
extractConsequenceEnrichmentComparison
extractConsequenceGenomeWide

Examples

### Prepare example data
data("exampleSwitchListAnalyzed")

### Summarize switch consequences
consequenceSummary <- extractConsequenceSummary(
    exampleSwitchListAnalyzed,
    returnResult = TRUE,        # return data.frame with summary
    plotGenes = TRUE            # plot summary
)

dim(consequenceSummary)

subset(consequenceSummary, featureCompared=='Domains identified')

kvittingseerup/IsoformSwitchAnalyzeR documentation built on June 28, 2024, 5:41 p.m.