group.exprs: Construct subunit-level expression data

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

Description

Split whole protein expression into the subunits.

Usage

group.exprs(exprs, ref = NULL)

Arguments

exprs	data.frame. Protein expression data where variables(genes / proteins) in the columns and samples in the rows.
ref	data.frame. Group information of the variables, e.g., protein complex. The table must include 'group_id'(group identifier, e,g., protein complex identifier),'desc'(description of the group,e.g., protein complex name),and 'varname'(variable name, e.g., proteins)

Value

list of which element corresponds to each complex.

• comp.exprs - data.frame. Variables (genes/proteins) in the columns and samples in the rows.

• comp.names - character vector. Complex names

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

Author(s)

Yusuke Matsui

References

Yusuke MATSUI et al.(2020) RoDiCE: Robust differential protein co-expression analysis for cancer complexome (submitted).

Examples

data(ccrcc.subset)
data(corum.subset)
tumor = ccrcc.subset$tumor
normal = ccrcc.subset$normal
tumorByComplex = group.exprs(tumor,corum.subset)
normalByComplex = group.exprs(normal,corum.subset)

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