create_sce_by_dir: create a SingleCellExperiment object from data folder...

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

create a SingleCellExperiment object from data folder generated by preprocessing step

Description

after we run sc_gene_counting and finish the preprocessing step. create_sce_by_dir can be used to generate the SingleCellExperiment object from the folder that contains gene count matrix and QC statistics. it can also generate the html report based on the gene count and quality control statistics

Usage

create_sce_by_dir(
  datadir,
  organism = NULL,
  gene_id_type = NULL,
  pheno_data = NULL,
  report = FALSE
)

Arguments

datadir	the directory that contains all the data and 'stat' subfolder.
organism	the organism of the data. List of possible names can be retrieved using the function 'listDatasets'from 'biomaRt' package. (i.e 'mmusculus_gene_ensembl' or 'hsapiens_gene_ensembl')
gene_id_type	gene id type of the data A possible list of ids can be retrieved using the function 'listAttributes' from 'biomaRt' package. the commonly used id types are 'external_gene_name', 'ensembl_gene_id' or 'entrezgene'
pheno_data	the external phenotype data that linked to each single cell. This should be an AnnotatedDataFrame object
report	whether to generate the html report in the data folder

Details

after we run sc_gene_counting and finish the preprocessing step. create_sce_by_dir can be used to generate the SingleCellExperiment object from the folder that contains gene count matrix and QC statistics.

Value

a SingleCellExperiment object

Examples

## Not run: 
# the sce can be created fron the output folder of scPipe
# please refer to the vignettes
sce = create_sce_by_dir(datadir="output_dir_of_scPipe",
    organism="mmusculus_gene_ensembl",
    gene_id_type="ensembl_gene_id")

## End(Not run)
# or directly from the gene count and quality control matrix:
data("sc_sample_data")
data("sc_sample_qc")
sce = SingleCellExperiment(assays = list(counts = as.matrix(sc_sample_data)))
organism(sce) = "mmusculus_gene_ensembl"
gene_id_type(sce) = "ensembl_gene_id"
QC_metrics(sce) = sc_sample_qc
demultiplex_info(sce) = cell_barcode_matching
UMI_dup_info(sce) = UMI_duplication
dim(sce)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.