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iblacksand / WebGestaltR

R package for WebGestalt
https://iblacksand.github.io/WebGestaltR/
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Multi-omics data input #3

Open iblacksand opened 1 year ago

iblacksand commented 1 year ago

Inputting multiple lists and gmts for the R-package may be cumbersome. We have to know what ID type each ID type is, to determine which GMTs are needed. For example, if there are no metabolites, we can just use the original GMT. Also the parameter names won't match for multiomics (i.e. interestGene should be interestLists). Either users will have to directly call WebGestaltRMultiomics or they will have to deal with parameter names not exactly matching.

Example

This is one example for how a user could provide multiple lists

genelists <- c("a.rnk", "b.rnk")
id_types <- c("gene_symbol", "hmdb")
db_type <- "KEGG"
WebGestaltRMultiomics(interestFiles = genelists, interestTypes = id_types, enrichDatabase = db_type, ...)
iblacksand commented 1 year ago

In a similar note, we may need to rename interestGene to interestList since it may not be a list of genes.

iblacksand commented 1 year ago

Additionally, we will have to add parameters for how to combine lists and how to normalize them.

iblacksand commented 1 year ago

The names for the normalization methods should be "Rank based" or "Value based".