analyzeCPC2: Import Result of External Sequence Analysis

In kvittingseerup/IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Import Result of External Sequence Analysis

Description

Allows for easy integration of the result of CPC2 (external sequence analysis of coding potential) in the IsoformSwitchAnalyzeR workflow. Please note that due to the 'removeNoncodinORFs' option we recommend using analyzeCPC2 before analyzePFAM and analyzeSignalP if you have predicted the ORFs with analyzeORF. This is an alternative to analyzing CPAT results with analyzeCPAT.

Usage

analyzeCPC2(
    switchAnalyzeRlist,
    pathToCPC2resultFile,
    codingCutoff = 0.5,
    removeNoncodinORFs,
    ignoreAfterBar = TRUE,
    ignoreAfterSpace = TRUE,
    ignoreAfterPeriod = FALSE,
    quiet=FALSE
)

Arguments

switchAnalyzeRlist	:A switchAnalyzeRlist object
pathToCPC2resultFile	: A string indicating the full path to the CPC2 result file. See details for suggestion of how to run and obtain the result of the CPAT tool.
codingCutoff	: Numeric indicating the cutoff used by CPC2 for distinguishing between coding and non-coding transcripts. The cutoff appears to be species independent. Default is 0.5.
removeNoncodinORFs	: A logic indicating whether to remove ORF information from the isoforms which the CPC2 analysis classifies as non-coding. This can be particular useful if the isoform (and ORF) was predicted de-novo but is not recommended if ORFs was imported from a GTF file. This will affect all downstream analysis and plots as both analysis of domains and signal peptides requires that ORFs are annotated (e.g. analyzeSwitchConsequences will not consider the domains (potentially) found by Pfam if the ORF have been removed).
ignoreAfterBar	A logic indicating whether to subset the isoform ids by ignoring everything after the first bar ("|"). Useful for analysis of GENCODE data. Default is TRUE.
ignoreAfterSpace	A logic indicating whether to subset the isoform ids by ignoring everything after the first space (" "). Useful for analysis of gffutils generated GTF files. Default is TRUE.
ignoreAfterPeriod	A logic indicating whether to subset the gene/isoform is by ignoring everything after the first period ("."). Should be used with care. Default is FALSE.
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: Use default parameters and if required select the most similar species. If the [webserver](http://cpc2.cbi.pku.edu.cn/batch.php) (batch submission) was used, download the tab-delimited result file (via the "Download the result" button). If a stand-alone version was just just supply the path to the result file.

Please note that the analyzeCPC2() function will automatically only import the CPC2 results from the isoforms stored in the switchAnalyzeRlist - even if many more are stored in the result file.

Value

Two columns are added to isoformFeatures: 'codingPotentialValue' and 'codingPotential' containing the predicted coding potential values and a logic indicating whether the isoform is coding or not respectively (based on the supplied cutoff).

Author(s)

Kristoffer Vitting-Seerup

References

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

• CPC2 : Kang et al CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 2017

See Also

createSwitchAnalyzeRlist
extractSequence
analyzePFAM
analyzeNetSurfP2
analyzeSignalP
analyzeCPAT
analyzeSwitchConsequences

Examples

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

### Add CPC2 analysis
exampleSwitchListAnalyzed <- analyzeCPC2(
    switchAnalyzeRlist   = exampleSwitchListIntermediary,
    pathToCPC2resultFile = system.file("extdata/cpc2_result.txt", package = "IsoformSwitchAnalyzeR"),
    removeNoncodinORFs   = TRUE   # because ORF was predicted de novo
)

exampleSwitchListAnalyzed

kvittingseerup/IsoformSwitchAnalyzeR documentation built on Jan. 14, 2024, 11:30 p.m.