guokai8/richr

Function Enrichment analysis and Network construction

richR

Description

richR provide functions richGO, richKEGG,and enrich to do functional enrichment analysis.

Installation

library(devtools)
install_github("guokai8/richR")

Quick tour

set.seed(123)   
library(richR)   
# To check the available species !!!
showData()   
# Make the GO and KEGG Pathway data for your analysis
# find suitable species name by using showensemble()    
hsago <- buildAnnot(species="human",keytype="SYMBOL",anntype = "GO")
hsako <- buildAnnot(species = "human",keytype="SYMBOL", anntype = "KEGG")

Support KEGG Module and MSIGDB anntation

hsamgi <- buildMSIGDB(species="human",keytype="SYMBOL",anntype="GO")
hsakom <- buildAnnot(species = "human",keytype="SYMBOL", anntype = "KEGGM")

---

You can make annotation data for all species from bioAnno package

• If had bioAnno installed, you can build annotation package with it

# library(bioAnno)
# fromKEGG(species="ath")
# athgo<-buildOwn(dbname="org.ath.eg.db",anntype="GO")  
# athko<-buildOwn(dbname="org.ath.eg.db",anntype="KEGG") 
# Please go over the bioAnno package webpage ("https://github.com/guokai8/bioAnno") to learn more

---

Simple example for enrichment analysis

gene <- sample(unique(hsago$GeneID),1000)
resgo <- richGO(gene,godata = hsago,ontology ="BP")
head(resgo)
ggbar(resgo,top = 20,usePadj = F)
###extract gene and related term
head(detail(resgo))

cluster GO enrichment result

resc<-richCluster(resgo)
ggdot(resc)

resko<-richKEGG(gene,hsako,pvalue=0.05)
head(resko)
ggdot(resko,top=10,usePadj = F)
##GSEA
set.seed(123)
hsako <- buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
name <- sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene) <- name
res <- richGSEA(gene,object = hsako)

Support DAVID analysis (Online)

gene <- sample(unique(hsako$GeneID),1000)
res <- richDAVID(gene,keytype="ENTREZID",species="human")

You can also get network graphic for any type of enrichment analysis result and also combine different enrichment result

ggnetplot(resko,top=20)
ggnetwork(resgo,top=20,weightcut = 0.01)

Directly support dplyr filter, select, mutate,group_by ... functions

library(dplyr)
filter(resko,Padj<0.05)%>%head()
select(resko,Term)

Generate figures with mutiple enrichment results for groups

gene1 <- sample(unique(hsako$GeneID),1000)
gene2 <- sample(unique(hsako$GeneID),1000)
resko1 <- richKEGG(gene1,kodata = hsako)
resko2 <- richKEGG(gene2,kodata = hsako)
res <- compareResult(list(S1=resko1,S2=resko2))
comparedot(res)

Generate figures with different enrichment results

ggnetmap(list(resgo,resko),top=50,visNet=TRUE,smooth=FALSE)

Contact information

For any questions please contact [email protected]

richr's Issues

featureRequest: ordering of items in bar/dot plots

Hi,

It would be great if users can specify how ggbar and ggdot order the items in the plots. Currently, the default is ordering by the name of the items (pathways, etc) or Rich factor (% in genome). It would be great if we can order by Padj as well.

Thanks,
Junguk

Intallation error

Hi,

I am unable to load the package. Here is the error: install_github("hurlab/richR") Downloading GitHub repo hurlab/richR@HEAD Error: Failed to install 'richR' from GitHub: (converted from warning) restarting interrupted promise evaluation

Could you please look into this? Thank in advance.

Best,
Aastha

richGSEA() parameter object -> annot

To be consistent with other functions,
it would be better to use annot instead of object.

Update is neede regarding distinct_()

Warning message:
distinct_() was deprecated in dplyr 0.7.0.
ℹ Please use distinct() instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the richR package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.