Write single cell counts from an indexed bam file
Usage
write_sc_counts_from_bam(
bam_file,
out_dir,
cell_names,
cell_suffix = NULL,
genome = NULL,
bin_size = 50000000,
overwrite = FALSE,
id = "",
description = "",
min_mapq = NULL,
samtools_bin = "samtools",
samtools_opts = NULL,
num_reads = NULL,
verbose = FALSE
)
scc_from_bam(
bam_file,
out_dir,
cell_names,
cell_suffix = NULL,
genome = NULL,
bin_size = 50000000,
id = "",
description = "",
min_mapq = NULL,
samtools_bin = "samtools",
samtools_opts = NULL,
num_reads = NULL,
verbose = FALSE,
overwrite = FALSE
)Arguments
- bam_file
name of the bam file
- out_dir
output directory.
- cell_names
a vector with the cell names or an ATAC object
- cell_suffix
a suffix to add to the cell names (optional). This is useful when you want to merge multiple batches of cells. The suffix would be added in the following way:
paste0(cell_name, "-", cell_suffix).- genome
genome name (e.g. hg19). Will be inferred from the ScPeaks object if provided
- bin_size
Size of the genomic bins to use (in bp). Each chromsome will be chunked into bins with size which is smaller than this value. Default is 50Mb.
- overwrite
overwrite existing directory (optional)
- id
an identifier for the object, e.g. "pbmc".
- description
description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)"
- min_mapq
minimal mapping quality (optional)
- samtools_bin
path to samtools executable
- samtools_opts
additional options for samtools (e.g. "--subsample 0.1")
- num_reads
number of reads (within the
region) to process (optional).- verbose
verbose output (optional)