DeComplex: Convert gene level differences to pathway level or complex...

In WubingZhang/rMAUPS: Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.

Convert gene level differences to pathway level or complex level differences.

Description

Convert gene level differences to pathway level or complex level differences.

Usage

DeComplex(
  depres,
  type = "GOBP+GOCC+CORUM+REACTOME",
  lfc = "log2FC",
  pval = "pvalue"
)

Arguments

depres	normalized count matrix; rows are all genes in the signature that shall be summarized into one score; columns are samples
type	Molecular signatures for testing, available datasets include Pathway (KEGG, REACTOME, C2_CP), GO (GOBP, GOCC, GOMF), MSIGDB (C1, C2 (C2_CP (C2_CP_PID, C2_CP_BIOCARTA), C2_CGP), C3 (C3_MIR, C3_TFT), C4, C6, C7, HALLMARK) and Complex (CORUM). Any combination of them are also accessible (e.g. 'GOBP+GOMF+KEGG+REACTOME').
lfc	Gene sets.
pval	("PC", default), Pearson, ssGSEA or mean (other value). fisher, stouffer.

Value

A list.

Author(s)

Wubing Zhang

WubingZhang/rMAUPS documentation built on March 21, 2022, 8:48 p.m.