load_bulk_US: Creates a SummarizedExperiment containing the estimated US...

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

Creates a SummarizedExperiment containing the estimated US counts for the bulk RNA-seq data

Description

load_bulk_US imports the bulk estimated US (Unspliced, and Spliced) counts (computed by salmon), and stores them into a SummarizedExperiment object.

Usage

load_bulk_US(path_to_quant_files, sample_ids)

Arguments

path_to_quant_files	a vector of length equals to the number of samples: each element indicates the path to the US estimated count matrix of the respective sample (i.e., quant.sf file).
sample_ids	a vector of length equals to the number of samples, indicating the names of the respective samples in 'path_to_quant_files'.

Value

A SummarizedExperiment object.

Author(s)

Simone Tiberi [e-mail]

See Also

load_bulk_EC, 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))

# US estimates:
quant_files = file.path(data_dir, "salmon", sample_ids, "quant.sf")
file.exists(quant_files)

# load US estimated counts:
SE = load_bulk_US(quant_files,
                  sample_ids)

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