topDSExons: Extract top differentially spliced exons
In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
This function is to extract top n differentially spliced exons, ranked by p-values or
NB-stats.
Usage
1
topDSExons(RCS, n = 20, sortBy = c("pvalue", "NBstat"))
Arguments
RCS
a ReadCountSet object after running DSpermutePval.
n
the number of top genes.
sortBy
indicating whether p-value or NBstat to be used for ranking genes.
Value
A table for top n exons. Columns include: geneID, exonID, testable, NBstat, pvalue, padjust, and meanCounts.
Author(s)
Xi Wang, xi.wang@newcastle.edu.au
See Also
Examples
1
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data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- estiExonNBstat(RCS_example)
RCS_example <- estiGeneNBstat(RCS_example)
RCS_example <- DSpermutePval(RCS_example, permuteMat)
topDSExons(RCS_example, 10, "NB")
sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
This function is to extract top n differentially spliced exons, ranked by p-values or NB-stats.
Usage
1 | topDSExons(RCS, n = 20, sortBy = c("pvalue", "NBstat"))
|
Arguments
RCS |
a ReadCountSet object after running |
n |
the number of top genes. |
sortBy |
indicating whether p-value or NBstat to be used for ranking genes. |
Value
A table for top n exons. Columns include: geneID, exonID, testable, NBstat, pvalue, padjust, and meanCounts.
Author(s)
Xi Wang, xi.wang@newcastle.edu.au
See Also
Examples
1 2 3 4 5 6 7 | data(RCS_example, package="SeqGSEA")
permuteMat <- genpermuteMat(RCS_example, times=10)
RCS_example <- exonTestability(RCS_example)
RCS_example <- estiExonNBstat(RCS_example)
RCS_example <- estiGeneNBstat(RCS_example)
RCS_example <- DSpermutePval(RCS_example, permuteMat)
topDSExons(RCS_example, 10, "NB")
|
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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