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

View source: R/analyze_switch_consequences.R

This functions analyzes for enrichment of specific consequnces by for each set of opposing consequnces (fx. domain gain vs loss), by analyzing the fraction of events belonging to one of them.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
extractConsequenceEnrichment(
switchAnalyzeRlist,
consequencesToAnalyze = 'all',
alpha=0.05,
dIFcutoff = 0.1,
countGenes = TRUE,
analysisOppositeConsequence=FALSE,
plot=TRUE,
localTheme = theme_bw(base_size = 12),
minEventsForPlotting = 10,
returnResult=TRUE,
returnSummary=TRUE
)
``` |

`switchAnalyzeRlist` |
A |

`consequencesToAnalyze` |
A string indicating which consequnces should be considered. See detail section of |

`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%). |

`countGenes` |
A logic indicating whether it is the number of genes (if TRUE) or isoform switches (if FALSE) which primarly result in gain/loss that are counted. Default is TRUE. |

`analysisOppositeConsequence` |
A logic indicating whether reverse the analysis meaing if "Domain gains"" are analyze using default parameters setting |

`plot` |
A logic indicting whether the analysis should be plotted. Default is TRUE. |

`localTheme` |
General ggplo2 theme with which the plot is made, see |

`minEventsForPlotting` |
The minimum number of events (total gain/loss) must be pressent before the result is visualized. Default is 10. |

`returnResult` |
A logic indicating whether the analysis should be returned as a data.frame. Default is TRUE. |

`returnSummary` |
A logic indicating whether to return the statistical summary (if TRUE) or the underlying data (if FALSE). Default is TRUE. |

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. Bioinformatics (2019).

`analyzeSwitchConsequences`

`extractSwitchSummary`

`extractConsequenceEnrichmentComparison`

`extractConsequenceGenomeWide`

1 2 3 4 | ```
### Load exampled data
data("exampleSwitchListAnalyzed")
extractConsequenceEnrichment( exampleSwitchListAnalyzed)
``` |

kvittingseerup/IsoformSwitchAnalyzeR documentation built on July 20, 2019, 8:54 a.m.

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