CreateSingleCellObject: Create SingleCellExperiment instance

In SaritaPoonia/unCTC: Characterising single circulating tumor cell transcriptomes

Create SingleCellExperiment instance

Description

Creating SingleCellExperiment instance of the data. Steps in creating SingleCellExperiment instance are like this. 1. Integrate all the data matrix passed in the list on the basois of common genes. 2. Filter out low quality data. 3. Use Linnorm.Norm function to remove batch effect between data taken from different experiments/bathes 4. Create SingleCellExperiment instances. In this instance two type of data format present.

Raw_filtered_data = Low quality gene and cell filtered out matrix without batch effect correction.

Usage

CreateSingleCellObject(data_list = list(), min_sample = 5, min_gene = 1500)

Arguments

data_list	List of expression matrix. Genes should be in rows and cells should be in columns in each data in the list.
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

Value

sce SingleCellExperimemnt instance od data passed in a list.

Examples

data1 = unCTC::Poonia_et_al._TPMData
data2 = unCTC::Ding_et_al._WBC1_TPMData
Data_list = list(data1,data2)
sce_obj = CreateSingleCellObject(data_list=Data_list,
                                  min_sample =5,
                                  min_gene=1500)

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