analyzeNetSurfP2 {IsoformSwitchAnalyzeR}R Documentation

Import Result of NetSurfP2 analysis

Description

Allows for easy integration of the result of NetSurfP2 (performing external sequence analysis which include Intrinsically Disordered Regions (IDR)) in the IsoformSwitchAnalyzeR workflow. This function also supports using a sliding window to extract IDRs. Please note that due to the 'removeNoncodinORFs' option in analyzeCPAT and analyzeCPC2 we recommend using analyzeCPC2/analyzeCPAT before using analyzeNetSurfP2, analyzePFAM and analyzeSignalP if you have predicted the ORFs with analyzeORF.

Usage

analyzeNetSurfP2(
    switchAnalyzeRlist,
    pathToNetSurfP2resultFile,
    smoothingWindowSize = 5,
    probabilityCutoff = 0.5,
    minIdrSize = 30,
    showProgress = TRUE,
    quiet = FALSE
)

Arguments

switchAnalyzeRlist

A switchAnalyzeRlist object

pathToNetSurfP2resultFile

A string indicating the full path to the NetSurfP-2 result file. Can be gziped.

smoothingWindowSize

An integer indicating how large a sliding window should be used to calculate a smoothed (via mean) disordered probability score of a particular position in a peptide. This has as a smoothing effect which prevents IDRs from not being detected (or from being split into sub-IDRs) by a single residue with low probability. The tradeoff is worse accuracy of detecting the exact edges of the IDRs. To turn of smoothing simply set to 1. Default is 5 amino acids.

probabilityCutoff

A doubble indicating the cutoff applied to the (smoothed) disordered probability score (see "smoothingWindowSize" argument above) for calling a residue as "disordered". The default, 30 amino acids, is an accepted standard for long IDRs.

minIdrSize

An integer indicating how long a strech of disordered amino acid constiture the "region" part of the Intrinsically Disordered Region definition. The default, 30 amino acids, is an accepted standard for long IDRs.

showProgress

A logic indicating whether to make a progress bar (if TRUE) or not (if FALSE). Default is TRUE.

quiet

A logic indicating whether to avoid printing progress messages (incl. progress bar). Default is FALSE

Details

Intrinsically Disordered Regions (IDR) are regions of a protein which does not have a fixed three-dimentional structure (oposite protein domains). Such regions are thought to play important roles in all aspects of biolgiy (and when it goes wrong) through multiple different functional aspectcs - including facilitating protein interactions.

The NetSurfP web-server currently have no restriction on the number of sequences in the file uploaded so we sugget using the combined aa fasta file. See extractSequence for info on how to split the amino acid fasta files.

Notes for how to run the external tools:
Use default paramters. If you want to use the webserver it is easily done as follows: 1) Go to http://www.cbs.dtu.dk/services/NetSurfP-2.0/ 2) Upload the amino acoid file (_AA) created with extractSequence. 3) Submit your job. 4) Wait till job is finished (if you submit your email you will recieve a notification). 5) In the top-right conor of the result site use the "Export All" botton to download the results as a CNV file. 6) Supply a string indicating the path to the downloaded cnv file directly to the "pathToNetSurfP2resultFile" argument.

If you run NetSurfP-2 locally just use the "–csv" argument and provide the resulting csv file to the pathToNetSurfP2resultFile argument.

IDR are only added to isoforms annotated as having an ORF even if other isoforms exists in the file. This means if you quantify the same isoform many times you can just run NetSurfP2 once on all isoforms and then supply the entire file to analyzeNetSurfP2.

Please note that the analyzeNetSurfP2() function will automatically only import the NetSurfP-2 results from the isoforms stored in the switchAnalyzeRlist - even if many more are stored in the result file.

Value

A colum called 'idr_identified' is added to isoformFeatures containing a binary indication (yes/no) of whether a transcript contains any protein domains or not. Furthermore the data.frame 'idrAnalysis' is added to the switchAnalyzeRlist containing positional data of each IDR identified.

The data.frame added have one row per isoform and contains the columns:

Author(s)

Kristoffer Vitting-Seerup

References

See Also

createSwitchAnalyzeRlist
extractSequence
analyzeCPAT
analyzeSignalP
analyzePFAM
analyzeSwitchConsequences

Examples

### Load example data (matching the result files also store in IsoformSwitchAnalyzeR)
data("exampleSwitchListIntermediary")
exampleSwitchListIntermediary

### Add NetSurfP-2 analysis
exampleSwitchListAnalyzed <- analyzeNetSurfP2(
    switchAnalyzeRlist = exampleSwitchListIntermediary,
    pathToNetSurfP2resultFile = system.file("extdata/netsurfp2_results.csv.gz", package = "IsoformSwitchAnalyzeR")
)

exampleSwitchListAnalyzed

[Package IsoformSwitchAnalyzeR version 1.6.0 Index]