Load scRNA-Ses count matrix into a Seurat object
load_sc_data.RdWrapper to load a cellranger counts output matrix into a Seurat object
Usage
load_sc_data(
data_path = NULL,
sample_name = NULL,
assay = "RNA",
gene_column = 2,
droplets_limit = 1e+05,
emptydrops_fdr = 0.001,
filter_replicates = TRUE,
BPPARAM = BiocParallel::SerialParam(),
my_seed = 1337L,
verbose = FALSE
)Arguments
- data_path
CHARACTER : pathway where the three cellranger files are stored (matrix, features and barcodes)
- sample_name
CHARACTER : sample name
- assay
CHARACTER : name of the assay corresponding to the initial input data (default to 'RNA')
- gene_column
NUMERIC : 1 (gene ID) or 2 (gene symbol), to be passed to the gene.column parameter in Seurat::Read10X function (default to 2)
- droplets_limit
INTEGER : max number of droplets to activate empty droplets filtering (default to 1E+05)
- emptydrops_fdr
INTEGER : False Discovery Rate to filter out empty droplets candidates (default to 1E+03)
- filter_replicates
LOGICAL : whether you want or not to group columns by barcode, in case of presence of duplicated barcode (default to TRUE)
- BPPARAM
an object of class DoparParam to be passed to BPPARAM parameter of DropletUtils::emptyDrops function. Could be generate by our create.parallel.instance function
- my_seed
INTEGER : seed to be used by DropletUtils::emptyDrops (default to 1337L)
- verbose
LOGICAL : whether to print messages or not (default to FALSE)