combine_omics: combine_omics
In biodataganache/leapR: Layered enrichment analysis of pathways R

combine_omics

R Documentation

combine_omics

Description

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

Usage

combine_omics(
  proteomics = NA,
  transcriptomics = NA,
  methylation = NA,
  cnv = NA,
  phospho = NA,
  proteomics_tag = "prot_",
  transcriptomics_tag = "txn_",
  methylation_tag = "meth_",
  cnv_tag = "cnv_",
  phospho_tag = "phospho_",
  id_column = NA
)

Arguments

`proteomics`	is a matrix of transcript values where rownames are ids and columns are conditions
`methylation`	is a matrix of methylation values where rownames are ids and columns are conditions
`phospho`	is a dataframe of phosphorylation data
`proteomics_tag`	is a text prefix to be added to protein ids
`transcriptomics_tag`	is a text prefix to be added to transcript ids
`methylation_tag`	is a text prefix to be added to methylation ids
`cnv_tag`	is a text prefix to be added to cnv ids
`phospho_tag`	is a text prefix to be added to phospho ids
`id_column`	is an optional column number for identifiers for the phospho data
`CNV`	is a matrix of copy number variant(CNV) values where rownames are ids and columns are conditions

Details

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

Examples

dontrun{
        library(leapr)

        # read in the example protein data
        data("protdata")
        # read in the example transcriptomics data
        data("transdata")
        
        # merge the two datasets by rows and add prefix tags for different omics types
        multi_omics = combine_omics(proteomics=protdata, transcriptomics=transdata)

}

biodataganache/leapR documentation built on Jan. 20, 2024, 2:55 a.m.