| Title: | RNA-seq data with different levels of gDNA contamination |
|---|---|
| Description: | Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination. |
| Authors: | Robert Castelo [aut, cre] (ORCID: <https://orcid.org/0000-0003-2229-4508>) |
| Maintainer: | Robert Castelo <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.12.0 |
| Built: | 2026-10-10 11:18:21 UTC |
| Source: | https://github.com/bioc/gDNAinRNAseqData |
This package provides access to RNA-seq BAM files containing different
levels of genomic DNA (gDNA) contamination.
LiYu22subsetBAMfiles(path = tempdir(), offline = FALSE) LiYu22phenoData(bamfiles)LiYu22subsetBAMfiles(path = tempdir(), offline = FALSE) LiYu22phenoData(bamfiles)
path |
(Default='tempdir()') Filesystem path where to store the BAM files. |
offline |
(Default='FALSE') If there is no internet connection, but the data has been previously downloaded, setting 'offline=TRUE' allows one to retrive the data from the ExperimentHub cache. |
bamfiles |
full filesystem paths to where the BAM files were downloaded with 'LiYu22subsetBAMfiles()'. |
Currently, this package allows one to download a subset of the data published in:
Li, X., Zhang, P., and Yu. Y. Gene expressed at low levels raise false discovery rates in RNA samples contaminated with genomic DNA. BMC Genomics, 23:554, 2022.
The subset of the data acccessible through this package corresponds to BAM files containing about 100,000 alignments sampled uniformly at random for the RNA-seq experiments produced from total RNA libraries mixed with different concentrations of gDNA, concretely 0% (no contamination), 1% and 10%; see Fig. 2 from Li et al. (2022).
'LiYu22subsetBAMfiles()' returns a string character vector of filesystem paths to the downloaded BAM files.
'LiYu22phenoData()' returns a 'data.frame' object with the gDNA contamination levels for the BAM files specified in the 'bamfiles' parameter, according to the publication by Li et al. (2022).
LiYu22subsetBAMfiles(): downloads the BAM files from the
RNA-seq data through the ExperimentHub, and returns the path in the
filesystem where the BAM files are stored.
LiYu22phenoData(): retrieves phenotypic data from the
BAM files downloaded with 'LiYu22subsetBAMfiles()'.
Li, X., Zhang, P., and Yu. Y. Gene expressed at low levels raise false discovery rates in RNA samples contaminated with genomic DNA. BMC Genomics, 23:554, 2022.
## for LiYu2subsetBAMfiles() bamfiles <- LiYu22subsetBAMfiles() bamfiles ## for LiYu22phenoData() bamfiles <- LiYu22subsetBAMfiles() LiYu22phenoData(bamfiles)## for LiYu2subsetBAMfiles() bamfiles <- LiYu22subsetBAMfiles() bamfiles ## for LiYu22phenoData() bamfiles <- LiYu22subsetBAMfiles() LiYu22phenoData(bamfiles)