combine_omics: combine_omics

In biodataganache/leapR: Layered enrichment analysis of pathways R

combine_omics

Description

Combine two or more omics matrices into one multi-omics matrix with 'tagged' ids.

Usage

combine_omics(omics_list, id_list = rep(NA, length(omics_list)))

Arguments

omics_list	List of ExpressionSet objects that contain the data to join with data type in the 'Annotation' slot
id_list	List of identifers to use, in the same order as the omics_list elements. If an element is 'NA', then rownames are used.

Details

This combines matrices of different omics types together and adds prefix tags to the ids.

Value

combined omics ExpressionSet

Examples

        library(leapR)


        pdata <- download.file('https://figshare.com/ndownloader/files/55781147',method='libcurl',destfile='protData.rda')
        load('protData.rda')
        p <- file.remove("protData.rda")
        
        tdata <- download.file("https://figshare.com/ndownloader/files/55781153",method='libcurl',destfile='transData.rda')
        load('transData.rda')
        p <- file.remove("transData.rda")
        
        phdata<-download.file('https://figshare.com/ndownloader/files/55781120',method='libcurl',destfile = 'phosData.rda')
        #phosphodata<-read.csv("phdata",check.names=FALSE,row.names=1)
        load('phosData.rda')
        p <- file.remove('phosData.rda')# read in the example protein data
        

        # merge the three datasets by rows and add prefix tags for different omics types
        multi_omics = combine_omics(list(pset, tset, phset), list(NA,NA,'hgnc_id'))

biodataganache/leapR documentation built on July 16, 2025, 11:10 p.m.