DSpermute4GSEA: Compute NB-statistics quantifying differential splicing on...
In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Description
Usage
Arguments
Details
Value
Note
Author(s)
References
See Also
Examples
Description
This function is to calculate NB-statistics quantifying differential splicing for each gene on each permutation data set.
The results will be used for GSEA run as DS background.
Usage
1
DSpermute4GSEA(RCS, permuteMat)
Arguments
RCS
a ReadCountSet object after running exonTestability.
permuteMat
a permutation matrix generated by genpermuteMat.
Details
Parallel running configuration: TODO
Value
A ReadCountSet object with slot permute_NBstat_gene updated.
Note
Please run exonTestability before run this function.
Author(s)
Xi Wang, xi.wang@newcastle.edu.au
References
Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.
See Also
exonTestability,
genpermuteMat,
DENBStatPermut4GSEA,
DSpermutePval
Examples
1
2
3
4
5
data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)
head(RCS_example@permute_NBstat_gene)
sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.
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Description Usage Arguments Details Value Note Author(s) References See Also Examples
Description
This function is to calculate NB-statistics quantifying differential splicing for each gene on each permutation data set. The results will be used for GSEA run as DS background.
Usage
1 | DSpermute4GSEA(RCS, permuteMat)
|
Arguments
RCS |
a ReadCountSet object after running |
permuteMat |
a permutation matrix generated by |
Details
Parallel running configuration: TODO
Value
A ReadCountSet object with slot permute_NBstat_gene updated.
Note
Please run exonTestability before run this function.
Author(s)
Xi Wang, xi.wang@newcastle.edu.au
References
Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.
See Also
exonTestability,
genpermuteMat,
DENBStatPermut4GSEA,
DSpermutePval
Examples
1 2 3 4 5 | data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)
head(RCS_example@permute_NBstat_gene)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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