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:

Author(s)

Kristoffer Vitting-Seerup

References

See Also

createSwitchAnalyzeRlist
extractSequence
analyzePFAM
analyzeCPAT
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 1.4.0 Index]