PathwayEnrichmentScore: Calculate Pathway enrichment score of all cells for all...

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

Calculate Pathway enrichment score of all cells for all pathways

Description

Calculate gene set enrichment across samples/cells using the GSVA package in R, a non-parametric method and unsupervised software programme.

Usage

PathwayEnrichmentScore(
  data_list = list(),
  data_id = list(),
  Genesets,
  min.size = 10,
  max.size = 500,
  min_Sample = 5,
  min_Gene = 1500,
  Parallel_threads = 4L
)

Arguments

data_list	List of gene expression data matricies. Genes/Features should be in rows and cells/ samples in columns.
data_id	List of names/ids of expression matrix
Genesets	list of genesets/pathways.
min.size	Minimum size of the resulting gene sets.
max.size	Maximum size of the resulting gene sets.
min_Sample	gene filter, filter out genes which are not expressed in at least min_Sample cells
min_Gene	cell filter, filter out those cells which do not express at least min_Gene genes
Parallel_threads	= Number of threads in parallel to execute process.

Value

PathwayData list of athway enrichment score and pathway metadata.

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,
                                        Genesets=Genesets,
                                        min.size=70,
                                        max.size=100,
                                        min_Sample = 5,
                                        min_Gene = 1500
                                        )

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