Here we show how to download a subset of the RNA-seq 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. https://doi.org/10.1186/s12864-022-08785-1
The subset of the data available through this package are BAM files
containing about 100,000 alignments, sampled uniformly at random from
complete BAM files. These complete BAM files were obtained by aligning
the RNA-seq reads sequenced 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). The original RNA-seq data is
publicly available at https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA007961
and you can find the pipeline to generate this subset of the data in the
file
gDNAinRNAseqData/inst/scripts/make-data_LiYu22subsetBAMfiles.R
stored in this package.
To download these subsetted BAM files, and the corresponding index
(.bai) files, we load this package and call the function
LiYu22subsetBAMfiles():
## [1] "/tmp/RtmpBfVnpA/s32gDNA0.bam" "/tmp/RtmpBfVnpA/s33gDNA0.bam"
## [3] "/tmp/RtmpBfVnpA/s34gDNA0.bam" "/tmp/RtmpBfVnpA/s26gDNA1.bam"
## [5] "/tmp/RtmpBfVnpA/s27gDNA1.bam" "/tmp/RtmpBfVnpA/s28gDNA1.bam"
## [7] "/tmp/RtmpBfVnpA/s23gDNA10.bam" "/tmp/RtmpBfVnpA/s24gDNA10.bam"
## [9] "/tmp/RtmpBfVnpA/s25gDNA10.bam"The previous function call can take a path argument to
specify the path in the filesystem where we would like to store the
downloaded BAM files, which by default is a temporary path from the
current R session; consult the help page of
LiYu22subsetBAMfiles() for full details.
We can also retrieve the gDNA concentrations associated to each BAM file with the following function call:
## gDNA
## s32gDNA0 0
## s33gDNA0 0
## s34gDNA0 0
## s26gDNA1 1
## s27gDNA1 1
## s28gDNA1 1
## s23gDNA10 10
## s24gDNA10 10
## s25gDNA10 10## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Rsamtools_2.28.0 Biostrings_2.80.2 XVector_0.52.0
## [4] GenomicRanges_1.64.0 IRanges_2.46.0 S4Vectors_0.50.3
## [7] Seqinfo_1.2.0 BiocGenerics_0.58.1 generics_0.1.4
## [10] gDNAinRNAseqData_1.12.0 BiocStyle_2.40.0
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.52.2 xfun_0.61 bslib_0.12.0
## [4] httr2_1.3.0 Biobase_2.72.0 vctrs_0.7.3
## [7] tools_4.6.1 bitops_1.1-0 curl_8.0.0
## [10] parallel_4.6.1 tibble_3.3.1 AnnotationDbi_1.74.0
## [13] RSQLite_3.53.3 blob_1.3.0 pkgconfig_2.0.3
## [16] dbplyr_2.6.0 lifecycle_1.0.5 compiler_4.6.1
## [19] codetools_0.2-20 htmltools_0.5.9 sys_3.4.3
## [22] buildtools_1.0.0 sass_0.4.10 RCurl_1.98-1.20
## [25] yaml_2.3.12 pillar_1.11.1 crayon_1.5.3
## [28] jquerylib_0.1.4 BiocParallel_1.46.0 cachem_1.1.0
## [31] ExperimentHub_3.2.2 AnnotationHub_4.2.2 tidyselect_1.2.1
## [34] digest_0.6.39 purrr_1.2.2 dplyr_1.2.1
## [37] BiocVersion_3.23.1 maketools_1.3.2 fastmap_1.2.0
## [40] cli_3.6.6 magrittr_2.0.5 XML_3.99-0.25
## [43] withr_3.0.3 filelock_1.0.3 rappdirs_0.3.4
## [46] bit64_4.8.6 rmarkdown_2.32 httr_1.4.9
## [49] bit_4.6.0 png_0.1-9 memoise_2.0.1
## [52] evaluate_1.0.5 knitr_1.52 BiocFileCache_3.2.0
## [55] rlang_1.3.0 glue_1.8.1 DBI_1.3.0
## [58] BiocManager_1.30.27 jsonlite_2.0.0 R6_2.6.1