In stephaniehicks/bodymapRat: Experimental dataset from the rat BodyMap project

require(knitr)
opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)

BiocStyle::markdown()

Introduction

The bodymapRat package contains gene expression data on 652 RNA-Seq samples from a comprehensive rat transcriptomic BodyMap study. These samples include the sequence identifier information provided in the header of the FASTQ files which can be used as a surrogate for batch. These samples have not been normalized or pre-processed.

The data are provided in a SummarizedExperiment. The phenotypic information can be extracted using the colData() function and a description of the phenotypic data is listed in the table below:

| Title | Description | | :--- | :--- | | sraExperiment | SRA Experiment ID | | title | Title of sample provided by the authors | | geoAccession | GEO Accession ID | | BioSample | BioSample ID | | avgLength | Average read length | | instrument | Machine identifier (from FASTQ header) | | runID | Run ID (from FASTQ header) | | fcID | Flow cell ID (from FASTQ header) | | fcLane | Flow cell lane (from FASTQ header) | | tile | Tile (from FASTQ header) | | xtile | xtile (from FASTQ header) | | ytile | ytile (from FASTQ header) | | organ | Body organ | | sex | Gender | | stage | Stage | | techRep | Technical replicate number | | colOrgan | Column of colors to help with plotting | | rnaRIN | RIN number | | barcode | barcode number |

The data can be accessed as follows:

library(SummarizedExperiment) 
library(bodymapRat)

We use the bodymapRat() function to download the relevant files from Bioconductor's ExperimentHub web resource. Running this function will download a SummarizedExperiment object, which contains read counts, as well as the metadata on the rows (genes) and columns (cells).

bm_rat <- bodymapRat()

# Get the expression data
counts = assay(bm_rat)
dim(counts)
counts[1:5, 1:5]

# Get the meta data along columns
head(colData(bm_rat))

The data in this package are used as an example data set in the qsmooth Bioconductor package.

References

1. Yu et al. (2013). A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nature Communications 5:3230. PMID: 24510058. PMCID: PMC3926002.

SessionInfo

sessionInfo()

stephaniehicks/bodymapRat documentation built on June 22, 2021, 6:32 a.m.