analyzeSignalP {IsoformSwitchAnalyzeR} | R Documentation |
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
.
analyzeSignalP( switchAnalyzeRlist, pathToSignalPresultFile, quiet=FALSE )
switchAnalyzeRlist |
A |
pathToSignalPresultFile |
A string indicating the full path to the summary SignalP result file. See |
quiet |
A logic indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE |
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
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.
Kristoffer Vitting-Seerup
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
createSwitchAnalyzeRlist
extractSequence
analyzePFAM
analyzeCPAT
analyzeSwitchConsequences
### Load example data data("exampleSwitchListIntermediary") exampleSwitchListIntermediary ### Add SignalP analysis exampleSwitchListAnalyzed <- analyzeSignalP( switchAnalyzeRlist = exampleSwitchListIntermediary, pathToSignalPresultFile = system.file( "extdata/signalP_results.txt", package = "IsoformSwitchAnalyzeR") ) exampleSwitchListAnalyzed