load_bulk_EC: Create a list containing the equivalence classes objects for...

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

Create a list containing the equivalence classes objects for the bulk RNA-seq data

Description

load_bulk_EC imports the bulk equivalence classes (computed by salmon), and stores them into a list.

Usage

load_bulk_EC(path_to_eq_classes = NULL, n_cores = NULL)

Arguments

path_to_eq_classes	a vector of length equals to the number of samples: each element indicates the path to the equivalence classes counts of the respective sample (i.e., aux_info/eq_classes.txt.gz file).
n_cores	the number of cores to parallelize the tasks on. Since parallelization is at the sample level (each sample is parallelized on a thread), we suggest setting n_cores to the number of sample, as set by default if 'n_cores' is not specified.

Value

A list object.

Author(s)

Simone Tiberi [e-mail]

See Also

load_bulk_US, DifferentialRegulation_bulk

Examples

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

# specify samples ids:
sample_ids = paste0("sample", seq_len(6))

# Equivalence classes:
equiv_classes_files = file.path(data_dir, "salmon", sample_ids, "aux_info/eq_classes.txt.gz")
file.exists(equiv_classes_files)

# load EC:
EC_list = load_bulk_EC(path_to_eq_classes = equiv_classes_files,
                       n_cores = 2)

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