analyzeSignalP {IsoformSwitchAnalyzeR} | R Documentation

## Import Result of SignalP Analysis

### Description

Allows for easy integration of the result of SignalP (external sequence analysis of signal peptides) in the IsoformSwitchAnalyzeR workflow. Please note that due to the 'removeNoncodinORFs' of the `analyzeCPAT` argument we recommend using `analyzeCPAT` before `analyzePFAM` and `analyzeSignalP` if you have predicted the ORFs with `analyzeORF`.

### Usage

    analyzeSignalP(
        switchAnalyzeRlist,
        pathToSignalPresultFile,
        quiet=FALSE
    )

### Arguments

`switchAnalyzeRlist` | A `switchAnalyzeRlist` object
`pathToSignalPresultFile` | A string indicating the full path to the summary SignalP result file. See `details` for suggestion of how to run and obtain the result of the SignalP tool.
`quiet` | A logic indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE

### Details

Notes for how to run the external tools: If using the web-server (http://www.cbs.dtu.dk/services/SignalP/) SignalP should be run with the paramter "standard" under "Output format" and "No graphics" under "Graphics output". When using a stand-alone version SignalP should be run with the '-f summary' option. If using the web-server the results should be copy pasted (from the web-page) into an empty plain text document (notepat, sublimetext TextEdit or similar (not word)) and save that to a txt file. This file is then used as input to the function. If a stand-alone version was just supply the path to the summary result file

### Value

A collum called 'signal_peptide_identified' is added to `isoformFeatures` containing a binary indiaction (yes/no) of whether a transcript contains a signal peptide or not. Furthermore the data.frame 'signalPeptideAnalysis' is added to the `switchAnalyzeRlist` containing the details of the signal peptide analysis.

The data.frame added have one row pr isoform and contains 6 columns:

- `isoform_id`: The name of the isoform analyzed. Matches the 'isoform_id' entry in the 'isoformFeatures' entry of the switchAnalyzeRlist

- `has_signal_peptide`: A text string indicating whether there is a signal peptide or not. Can be yes or no

- `network_used`: A text string indicating whether SignalP used the Neural Network (NN) optimized for proteins with trans-membrane sections (string='TM') or proteins without trans-membrane sections (string='noTM'). Per default, SignalP 4.1 uses the NN with TM as a preprocessor to determine whether to use TM or noTM in the final prediction (if 4 or more positions are predicted to be in a transmembrane state, TM is used, otherwise SignalP-noTM). Refrence: http://www.cbs.dtu.dk/services/SignalP/instructions.php

- `aa_removed`: A integer giving the number of amino acids removed when the signal peptide is cleaved off.

- `transcriptClevageAfter`: The transcript position of the last nucleotide in the isoform which is removed when the signal peptide is cleaved off.

- `genomicClevageAfter`: The genomic position of the last nucleotide in the isoform which is removed when the signal peptide is cleaved off.

### Author(s)

Kristoffer Vitting-Seerup

### References

- `This function` : Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

- `SignalP` : Petersen et al. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods, 8:785-786, 2011

### See Also

`createSwitchAnalyzeRlist`
`extractSequence`
`analyzeSwitchConsequences`

### Examples

    ### Load example data
    data("exampleSwitchListIntermediary")
    exampleSwitchListIntermediary

    ### Add SignalP analysis
    exampleSwitchListAnalyzed <- analyzeSignalP(
        switchAnalyzeRlist       = exampleSwitchListIntermediary,
        pathToSignalPresultFile = system.file(
            "extdata/signalP_results.txt",
            package = "IsoformSwitchAnalyzeR")
        )

    exampleSwitchListAnalyzed

[Package IsoformSwitchAnalyzeR version 1.2.0 Index]