Load multiple peak counts files into a SingleCellExperiment object

Load multiple named 3-column counts.tab.gz files from polyApipe.py into a SingleCellExperiment for analysis. Each cell will be uniquely named, and colData will include the batch.

load_peaks_counts_files_into_sce(
  counts_file_list,
  batch_names,
  peak_info_file,
  output,
  replace = FALSE,
  ...
)

Arguments

counts_file_list	A vector of tab-delimeted files of read counts per peak. The '<sample>.tab.gz' as output from polyApipe.py. Format: <peak> <cell> <count>
batch_names	A vector of the batch/sample names, in same order as counts_file_list
peak_info_file	GTF formatted peak file _specfically_ as output from polyApipe.py
output	Where to save the sce object on disk using saveHDF5SummarizedExperiment. Should not exist. This directory will be created.
replace	Overwrite existing output file? (Default=FALSE)
...	Other parameters passed through to *load_peaks_counts_into_sce* e.g. n_max, min_reads_per_barcode (but not cell_prefix or missing_peaks_are_zero)

See also

Other peak counts loading functions: load_peaks_counts_dir_into_sce(), load_peaks_counts_into_sce()

Examples

if (FALSE) {

counts_file1   <- system.file("extdata", "demo_dataset/demo_counts/SRR5259354_demo.tab.gz", package = "polyApiper")
counts_file2   <- system.file("extdata", "demo_dataset/demo_counts/SRR5259422_demo.tab.gz", package = "polyApiper")
peak_info_file <- system.file("extdata", "demo_dataset/demo_polyA_peaks.gff", package = "polyApiper") 

sce <- load_peaks_counts_files_into_sce(c(counts_file1,counts_file2),
               batch_names    = c("demo1","demo2"),
               peak_info_file = peak_info_file,
               output = "demo1and2")

}