bioMap: bioMap

In llrs/STATegRa: Classes and methods for multi-omics data integration

Description

Function to generate a bioMap object.

Usage

bioMap(name, metadata, map)

Arguments

name	Name to assign the object
metadata	A list with information of the mapping. Elements expected in the list are: (1) "type_v1" and "type_v2", refer to the nature of the features mapped; a vocabulary we recommend is "gene", "mRNA", "miRNA", "proteins", etc. (2) "source_database", provides information on the source of the mapping; from a specific data-base e.g. "targetscan.Hs.eg.db" to a genomic location mapping. (3) "data_extraction" stores information on the data the mapping was generated or downloaded.
map	A data.frame object storing the mapping. The data.frame may inclue an unlimited number of columns, however the first column must be named "Var1" and refer to the elements of "type_v1" and simmilarly for the second column ("Var2", "type_v2").

Value

An object of class bioMap

Author(s)

David Gomez-Cabrero

Examples

data(STATegRa_S2)
map.gene.miRNA<-bioMap(name = "Symbol-miRNA",
                       metadata = list(type_v1="Gene",type_v2="miRNA",
                                       source_database="targetscan.Hs.eg.db",
                                       data_extraction="July2014"),
                       map=mapdata)

llrs/STATegRa documentation built on May 29, 2019, 3:42 a.m.