parse.corum: Parsing protein complex information from CORUM.

In ymatts/RoDiCE: Robust differential co-expression test by copula

Description

This function parse the dataset from CORUM (ver.3.0) to obtain protein membership to protein copmlexes.

Usage

parse.corum(organism = "Human")

Arguments

organism

Single character vector. Select from: "Human",Mouse","Pig","Bovine","Rat","Mammalia","Rabbit","Dog","Hamster" "MINK"

Details

The data is complied from CORUM The resulting output can be used for 'ref' object in netvis() function.

Value

list consists of:

• comp.tbl - data.frame. It is consisting from complexID(complex identifier given in CORUM database), group_id(complex name),varname(subunit).

• comp.list - list version of comp.tbl. Each list elements corresponds to a complex.

• comp.raw - data.frame. Raw data from CORUM database "allComplexes.txt" from http://mips.helmholtz-muenchen.de/corum/#download.

References

Giurgiu, M. et al. (2019) CORUM: the comprehensive resource of mammalian protein complexes-2019. Nucleic Acids Res, 47(D1), D559–D563.

Examples

ref = parse.corum("Human")
names(ref)

ymatts/RoDiCE documentation built on Jan. 1, 2021, 1:45 p.m.