analyzeAlternativeSplicing {IsoformSwitchAnalyzeR}R Documentation

Analyse alternative splicing (including intron retention(s))

Description

These function utilize the analysis of alternative splicing previously implemented in the now decapitated spliceR package which compares each isoform in a gene to the hypothetical pre-RNA generated by combining all the exons within a gene and classify the changes in alternative splicing.

Usage

analyzeAlternativeSplicing(
    switchAnalyzeRlist,
    onlySwitchingGenes=TRUE,
    alpha=0.05,
    dIFcutoff = 0.1,
    showProgress=TRUE,
    quiet=FALSE
)

analyzeIntronRetention(
    switchAnalyzeRlist,
    onlySwitchingGenes = TRUE,
    alpha = 0.05,
    dIFcutoff = 0.1,
    showProgress = TRUE,
    quiet = FALSE
)

Arguments

switchAnalyzeRlist

A switchAnalyzeRlist object.

onlySwitchingGenes

A logic indicating whether to only analyze genes with isoform switches (as indicated by the alpha and dIFcutoff parameters). Default is FALSE.

alpha

The Cutoff used on the FDR correct p-values (q-values) for calling significance. Default is 0.05.

dIFcutoff

Cutoff used for minimum changes in (absolute) isoform usage before an isoform is considered eligible for switch testing. This cutoff can remove cases where isoforms with extremely low IF values are deemed significant and thereby included in the downstream analysis. This cutoff is analogous to having a (log2) fold change in a normal differential expression analysis of genes to ensure the DE genes have a certain effect size. Default is 0.1 (10%).

showProgress

A logic indicating whether to make a progress bar (if TRUE) or not (if FALSE). Default is TRUE.

quiet

A logic indicating whether to avoid printing progress messages. Default is FALSE

Details

The analyzeIntronRetention() is just a convinient wrapper for the analyzeIntronRetention() function to ensure backward compatability.

Alternative splicing (including alternative transcroption start sites (ATSS) and alternative transcription termination sites (ATTS)) are classified for each isoform comparing that isoform to the hypothetical pre-RNA generated by combining all the exons (after exclusion of retained introns) within a gene. Retained introns is defined as when one "exon" of one isoform overlaps two seperate exons in other isoform.

Since the comparison is to the hypothetical pre-RNA the interpretation of an event is as follows:

Value

A switchAnalyzeRlist where the collumn IR indicating the number of Intron Retentions found in each transcript have been added to the isoform_features entry. NA is used if the transcript was not analyzed. Furthermore a data.frame (called 'AlternativeSplicingAnalysis'), where for each isoform_id containing the number of alternative splicing events found as well as the genomic coordinates of the affected region(s), is added to the switchAnalyzeRlist.

Author(s)

Kristoffer Vitting-Seerup

References

See Also

extractSplicingSummary
extractSplicingEnrichment
extractSplicingEnrichmentComparison
extractSplicingGenomeWide

Examples

### Load data
data("exampleSwitchListIntermediary")

### Perform analysis
exampleSwitchListAnalyzed <- analyzeAlternativeSplicing(exampleSwitchListIntermediary, quiet=TRUE)

### Inspect result
head(exampleSwitchListAnalyzed$AlternativeSplicingAnalysis) # the first 6 does not have any intron retentions (IR)
table(exampleSwitchListAnalyzed$AlternativeSplicingAnalysis$IR) # there appear to be 7 transcripts that have an intron retention

[Package IsoformSwitchAnalyzeR version 1.4.0 Index]