load_USA: Creates a SingleCellExperiment containing the estimated USA...

In SimoneTiberi/DifferentialRegulation: Differentially regulated genes from scRNA-seq data

Creates a SingleCellExperiment containing the estimated USA counts for the single-cell RNA-seq data

Description

load_USA imports the single-cell estimated USA (Unspliced, Spliced and Ambiguous) counts (computed by alevin-fry), and stores them into a SingleCellExperiment object.

Usage

load_USA(path_to_counts, path_to_cell_id, path_to_gene_id, sample_ids)

Arguments

path_to_counts	a vector of length equals to the number of samples: each element indicates the path to the USA estimated count matrix of the respective sample (i.e., quants_mat.mtx file).
path_to_cell_id	a vector of length equals to the number of samples: each element indicates the path to the cell ids of the respective sample (i.e., quants_mat_rows.txt file).
path_to_gene_id	a vector of length equals to the number of samples: each element indicates the path to the gene ids of the respective sample (i.e., quants_mat_cols.txt file).
sample_ids	a vector of length equals to the number of samples: each element indicates the name of the sample.

Value

A SingleCellExperiment object.

Author(s)

Simone Tiberi [e-mail]

See Also

load_EC, DifferentialRegulation

Examples

# load internal data to the package:
data_dir = system.file("extdata", package = "DifferentialRegulation")

# specify samples ids:
sample_ids = paste0("organoid", c(1:3, 16:18))
# set directories of each sample input data (obtained via alevin-fry):
base_dir = file.path(data_dir, "alevin-fry", sample_ids)
file.exists(base_dir)

# set paths to USA counts, cell id and gene id:
# Note that alevin-fry needs to be run with `--use-mtx` option
# to store counts in a `quants_mat.mtx` file.
path_to_counts = file.path(base_dir,"/alevin/quants_mat.mtx")
path_to_cell_id = file.path(base_dir,"/alevin/quants_mat_rows.txt")
path_to_gene_id = file.path(base_dir,"/alevin/quants_mat_cols.txt")

# load USA counts:
sce = load_USA(path_to_counts,
               path_to_cell_id,
               path_to_gene_id,
               sample_ids)

SimoneTiberi/DifferentialRegulation documentation built on Feb. 5, 2024, 8:48 a.m.