extractSubCellShifts: Global overview of sub-cellular location changes
In kvittingseerup/IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

extractSubCellShifts

R Documentation

Global overview of sub-cellular location changes

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

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

`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().

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.

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).