overrepresentationAnalysis: Overrepresentation analysis
In JoWatson2011/phosphoRWHN: Random Walk on Heterogeneous Network For Functional Analysis of Phosphoproteomics Data
Description
Usage
Arguments
Value
View source: R/overrepresentationAnalysis.R
Description
Overrepresentation analysis
Usage
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overrepresentationAnalysis(
clustering,
database = "GO_Biological_Process_2018",
simplify = T,
vis = F,
colours = c(low = "#439981", high = "#b2d4cd"),
RWHN_sig = NULL
)
Arguments
clustering
A named vector; names correspond to sites in format Gene name_AminoAcid+Position (e.g. MAPK1_T185), values correspond to cluster. This is
database
Annotation database to calculate enrichment from. See enrichR website
simplify
If database = "GO_Biological_Process_2018", remove redundant terms
vis
logical; visualise output?
colours
if vis = T, a character vector of length 2 for colour scale
RWHN_sig
optional; results of RWHN if wanting to perform comparison,
Value
If vis = T, a ggplot object. If vis = F, a data frame containing enriched terms.
JoWatson2011/phosphoRWHN documentation built on Jan. 28, 2022, 4:02 a.m.
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Description Usage Arguments Value
View source: R/overrepresentationAnalysis.R
Description
Overrepresentation analysis
Usage
1 2 3 4 5 6 7 8 | overrepresentationAnalysis(
clustering,
database = "GO_Biological_Process_2018",
simplify = T,
vis = F,
colours = c(low = "#439981", high = "#b2d4cd"),
RWHN_sig = NULL
)
|
Arguments
clustering |
A named vector; names correspond to sites in format Gene name_AminoAcid+Position (e.g. MAPK1_T185), values correspond to cluster. This is |
database |
Annotation database to calculate enrichment from. See enrichR website |
simplify |
If database = "GO_Biological_Process_2018", remove redundant terms |
vis |
logical; visualise output? |
colours |
if vis = T, a character vector of length 2 for colour scale |
RWHN_sig |
optional; results of RWHN if wanting to perform comparison, |
Value
If vis = T, a ggplot object. If vis = F, a data frame containing enriched terms.
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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