GroupsDiffPathways: Claculate differential pathways between two type of groups.

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

Claculate differential pathways between two type of groups.

Description

Calculate top most differenciated upregulated pathways with significant p-value between in group1, given in the form of vector. Limma is used for differentiaition

Usage

GroupsDiffPathways(
  Pathway_mat,
  group,
  p_val = 0.05,
  lfc = 0,
  up_pathways_number = 10
)

Arguments

Pathway_mat	Pathway enrichment score matrix in which cells in the columns and pathways in the rows.
group	Different groups in a vector of size equals to the sample size of Pathway_mat
p_val	Threshold p value, default is 0.05
lfc	Threshold log fold change value, default is 0
up_pathways_number	select number of upregulated pathways in each group

Value

Up_pathway_mat return expression matrix of 10 and 100 most upregulated pathways respectively

Examples

data = unCTC::Poonia_et_al._TPMData
genesets = unCTC::c2.all.v7.2.symbols
Pathways_mat = PathwayEnrichmentScore(data_list=list(data),
                                       data_id = list("data"),
                                       Genesets = genesets,
                                       min.size = 50,
                                       max.size = 100)
groups = c(rep("TNBC",11),rep("NonTNBC",61))
output = GroupsDiffPathways(Pathway_mat=Pathways_mat$Pathway_score,
                          group=groups)

SaritaPoonia/unCTC documentation built on Nov. 8, 2022, 12:07 p.m.