extractSubCellShifts: Global overview of sub-cellular location changes

View source: R/tools.R

extractSubCellShiftsR Documentation

Global overview of sub-cellular location changes

Description

Extract summary of how sub-celluar locations have changed due to isoform switches.

Usage

extractSubCellShifts(
    switchAnalyzeRlist,
    plotGenes = TRUE,
    locationMinGenes = 3,
    returnResult = FALSE,
    localTheme = theme_bw()
)

Arguments

switchAnalyzeRlist

A switchAnalyzeRlist object where analyzeSwitchConsequences() have been run to identify consequences of isoform switches

plotGenes

A logic indicating whether to plot number of genes (if TRUE) or isoform switches (if FALSE). Default is TRUE.

locationMinGenes

An integer determining the minimum number of genes in a sub-cell location before it is plottet. Default is 3.

returnResult

A logic indicating whether the analysis should be returned as a data.frame. If FALSE a ggplot2 object will be returned instead. Default is FALSE.

localTheme

General ggplot2 theme with which the plot is made, see ?ggplot2::theme for more info. Default is theme_bw().

Value

If returnResult=FALSE a plot summarizing switches.

If returnResult=TRUE a data.frame with the summary for each comparison. This data.frame will have the following collumns:

  • condition_1: Condition 1.

  • condition_2: Condition 2.

  • location_gain: The location gained. Is "None if no location was lost"

  • location_loss: The location Lost. Is "None if no location was lost"

  • n_switch: The number of isoform switches with the location change.

  • n_genes: The number of genes containing isoform switche(s) with the location change.

Author(s)

Kristoffer Vitting-Seerup

References

  • 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).

See Also

analyzeSwitchConsequences


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