sc_integrate: Integrate multi-omic scRNA-Seq and scATAC-Seq data into a...

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

Integrate multi-omic scRNA-Seq and scATAC-Seq data into a MultiAssayExperiment

Description

Generates an integrated SCE object with scRNA-Seq and scATAC-Seq data produced by the scPipe pipelines

Usage

sc_integrate(
  sce_list,
  barcode_match_file = NULL,
  sce_column_to_barcode_files = NULL,
  rev_comp = NULL,
  cell_line_info = NULL,
  output_folder = NULL
)

Arguments

sce_list	A list of SCE objects, named with the corresponding technologies
barcode_match_file	A .csv file with columns corresponding to the barcodes for each tech
sce_column_to_barcode_files	A list of files containing the barcodes for each tech (if not needed then give a 'NULL' entry)
rev_comp	A named list of technologies and logical flags specifying if reverse complements should be applyed for sequences (if not needed then provide a 'NULL' entry)
cell_line_info	A list of files, each of which contains 2 columns corresponding to the barcode and cell line for each tech (if not needed then provide a 'NULL' entry)
output_folder	The path to the output folder

Value

Returns a MultiAssayExperiment containing the scRNA-Seq and scATAC-Seq data produced by the scPipe pipelines

Examples

## Not run: 
sc_integrate(
   sce_list = list("RNA" = sce.rna, "ATAC" = sce.atac),
   barcode_match_file = bc_match_file,
   sce_column_to_barcode_files = list("RNA" = rna_bc_anno, "ATAC" = NULL),
   rev_comp = list("RNA" = FALSE, "ATAC" = TRUE),
   cell_line_info = list("RNA" = rna_cell_line_info, "ATAC" = atac_cell_line_info,)
   output_folder = output_folder
   )

## End(Not run)  

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