Stouffer_score: Calculate Stouffer's Score for specific list of genes and...

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

Calculate Stouffer's Score for specific list of genes and plot stouffer's score between different type of cells.

Description

Calculate Stouffer,s score of genes passed as gene_list in Stouffer_score()

Usage

Stouffer_score(
  data_list = list(),
  min_Sample = 5,
  min_Gene = 1500,
  gene_list = list(),
  data_id = list(),
  MetaData = list(),
  metaColPos = 1,
  metaColName = "Class",
  Groupby = "Clusters",
  DDLKCluster_data
)

Arguments

data_list	List of expression matrix
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
gene_list	Vector of specific genes for which we want to calculate Stouffer's score
data_id	List of names/ids of expression matrix
MetaData	Optional, List of metadata of expression matricies in same order in which expression matricies in data_list, Column number and names of all the MetaData in the list must be same
metaColPos	column position in MetaData according to which we want to group data, default is 1
metaColName	Name of the column in MetaData according to which we want to group data, default is "Class"
Groupby	column name in MetaData according to which data is grouped.
DDLKCluster_data	output of DDLK_Clust.R method

Value

genes_Stouffer_score1 Cell wise stouffer score with Class info

Examples

data1 = unCTC::Poonia_et_al._TPMData
data2 = unCTC::Ding_et_al._WBC1_TPMData
Data_list = list(data1,data2)
Data_Id = list("data1","data2")
#LincrNA specific gene list
gene_list = unCTC::Breast_elevated_genes
S = Stouffer_score(data_list=Data_list,
                    min_Sample = 5,
                    min_Gene = 1500,
                    gene_list = gene_list,
                    Groupby = "data_id",
                    data_id= Data_Id)

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