Reference Sets

[Charline Jnnt]

Hi, 

Where can I found the reference sets used in WebGestalt.org, please ? 

I tried to run the WebGestaltRMultiOmics() function but it seems that I have to provide my own Reference list. However, I want to use your Reference files displayed in the web tool. ("genome", "KEGG",...) 

Compared to the WebGestaltR() function, the referenceSet argument is not available in the previous function...

Thank you,

[John Elizarraras]

Hello,

Thank you for reporting this issue. I didn't intend for this feature to be removed, but I will work on updating the package so this is available. If you would like, I can just provide you the reference files for now so that you don't have to wait. What lists would you like to use, and for what analyte type are they for (i.e. genome is gene/protein, KEGG is metabolite)?

Best,

John

[John Elizarraras]

This should be fixed now. You can reinstall the R Package to add the referenceSets parameter.

# install.packages("devtools") # run if devtools not already installed

devtools::install_github("bzhanglab/WebGestaltR")

Example code for using the referenceSets parameter can be seen below:

library("WebGestaltR")

analyte_lists <- c("data/genes.txt","data/metabolite.txt")

analyte_types <- c("entrezgene", "hmdb")

referenceSets <- c("genome", "KEGG")

db <- "pathway_KEGG"

method = "ORA"

listNames <- c("gene", "metabolite")

WebGestaltRMultiOmics(enrichMethod = method, analyteListFiles = analyte_lists, analyteTypes = analyte_types,

    enrichDatabase = db, referenceSets = referenceSets, projectName = "ORATEST", listNames = listNames,

    sigMethod = "top", topThr = 50)

[Charline Jnnt]

Hello, 

Thank you for your prompt reply, it's working fine now !

To know, I have reinstalled the R package as you said and functions work but It seems that the WebGestaltR.rdb is corrupt in the help directory:

```

Error in fetch(key): lazy-load database '~MyLibPath/WebGestaltR/help/WebGestaltR.rdb' is corrupt

```

Best