Differential_pathways: Calculate differential pathways between cells/clusters.

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

Calculate differential pathways between cells/clusters.

Description

Provide differential pathways between given groups.

Usage

Differential_pathways(
  Pathway_score,
  DDLK_Clusters,
  DifferentiateBy = "Clusters",
  p_val = 0.05,
  lfc = 0,
  up_pathways_number = 10
)

Arguments

Pathway_score	Output of PathwayEnrichmentScore.R method
DDLK_Clusters	Output of DDLK_Clust.R method
DifferentiateBy	Any column name from DDLK_Clusters$PathwayDDLK_clust, default is "Clusters"
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

Diff_Pathways list of three objects 1. DiffMatpathway = Pathway matrix with top most up_pathways_number differential pathways in each group 2. Diffup_pathways = top most up_pathways_number differential pathways in each group 3. annotations = Cell wise annotation of DifferentialMatrix

Examples

data1 = unCTC::Poonia_et_al._TPMData
data2 = unCTC::Ding_et_al._WBC1_TPMData
Data_list = list(data1,data2)
Data_Id = list("data1","data2")
Genesets = unCTC::c2.all.v7.2.symbols
Pathway_score = PathwayEnrichmentScore(data_list=Data_list,
                                        data_id= Data_Id,
                                         min_Sample = 5,
                                         min_Gene = 1500,
                                        Genesets=Genesets,
                                        min.size=70,
                                        max.size=100)

DDLK_Clusters = DDLK_Clust(PathwayScore = Pathway_score$Pathway_score,
                           PathwayMetaData=Pathway_score$Pathway_metadata,
                            n=3,
                            out.dir = paste0(getwd(),"/unCTC"))

Output = Differential_pathways(Pathway_score=Pathway_score,
                              DDLK_Clusters=DDLK_Clusters,
                              DifferentiateBy = "Clusters")

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