analyzeAlternativSplicing: Analyse alternative splicing (including intron retention(s))

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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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 convenient wrapper for the analyzeIntronRetention() function to ensure backward compatibility.

Alternative splicing (including alternative transcription 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 separate 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 column 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. In this data.frame genomic coordinates for each splice event are separated by ";" except for cases where there are multiple MES, then each set of coordinates belonging to a MES is separated by ',' (and then the coordinates belong to a specific MES is separated by ';').

Author(s)

Kristoffer Vitting-Seerup

References

See Also

extractSplicingSummary
extractSplicingEnrichment
extractSplicingEnrichmentComparison
extractSplicingGenomeWide

Examples

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### 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

kvittingseerup/IsoformSwitchAnalyzeR documentation built on Oct. 20, 2019, 1:41 p.m.