convertGMT: Convert gmt formatted pathway file to the Pathway ID, Entrez,...
In NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
Description
Usage
Arguments
Value
Description
Convert gmt formatted pathway file to the Pathway ID, Entrez, symbol
formatted data frame
Usage
1
convertGMT(gmtName, org_assembly, isSymbol = FALSE)
Arguments
gmtName
Custom pathway gmt file
org_assembly
Genome assembly of interest for the analysis. Possible
assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat,
"dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and
"hg38" for human
isSymbol
Boolean variable that hold the gene format of the gmt file.
If it is set as TRUE, gene format of the gmt file should be symbol.
Otherwise, gene format should be ENTREZ ID. By default, it is FALSE.
Value
return data frame
NoRCE documentation built on Nov. 8, 2020, 7:17 p.m.
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Description Usage Arguments Value
Description
Convert gmt formatted pathway file to the Pathway ID, Entrez, symbol formatted data frame
Usage
1 | convertGMT(gmtName, org_assembly, isSymbol = FALSE)
|
Arguments
gmtName |
Custom pathway gmt file |
org_assembly |
Genome assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human |
isSymbol |
Boolean variable that hold the gene format of the gmt file. If it is set as TRUE, gene format of the gmt file should be symbol. Otherwise, gene format should be ENTREZ ID. By default, it is FALSE. |
Value
return data frame
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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