1 Introduction

Welcome to the smokingMouse project. In this vignette we’ll show you how to access the smokingMouse LIBD datasets . You can find the analysis code and the data generation in here.

1.1 Motivation

The main motivation to create this bioconductor package was to provide public and free access to all RNA-seq datasets that were generated for the smokingMouse project, containing many variables of interest that make it possible to answer a wide range of biological questions related to smoking and nicotine effects in mice.

1.2 Overview

This bulk RNA-sequencing project consisted of a differential expression analysis (DEA) involving 4 data types: genes, exons, transcripts and junctions. The main goal of this study was to explore the effects of prenatal exposure to maternal smoking and nicotine exposures on the developing mouse brain. As secondary objectives, this work evaluated: 1) the affected genes by each exposure on the adult female brain in order to compare offspring and adult results and 2) the effects of smoking on adult blood and brain to search for overlapping biomarkers in both tissues. Finally, DEGs identified in mice were compared against previously published results from a human study (Semick, S.A. et al. (2018)).

The next table summarizes the analyses done at each level.

Table 1: 1. Data preparation: in this first step, counts of genes, exons and junctions were normalized to CPM and scaled; transcript expression values were only scaled since they were already in TMP. Then, low-expression features were removed using the indicated methods and samples were separated by tissue and age in order to create subsets of the data for downstream analyses. 2. Exploratory Data Analysis: QC metrics of the samples were examined and used to filter them; sample level effects were explored through dimensionality reduction methods and rare samples in PCA plots were manually removed from the datasets; gene level effects were evaluated with analyses of explanatory variables and variance partition. 3. Differential Expression Analysis: with the relevant variables identified in the previous steps, the DEA was performed at the gene level for nicotine and smoking, adult and pup, and blood and brain samples, and for 3 models: the naive one modeled ~Group + batch effects, the adjusted model modeled ~Group + Pregnancy + batch effects for adults and ~Group + Sex + batch effects for pups, and the interaction model ~Group*Pregnancy + batch effects for adults and ~Group*Sex + batch effects for pups; DEA on the rest of the levels was performed for pups only and using the adjusted model. After that, signals of the features in nicotine and smoking were compared, as well as the signals of exons and txs vs the effects of their genes, and genes’ signals were additionally compared in the different tissues, ages, models and species (vs human data of a previous study). All resultant DEG and DE features (and their genes) were quantified and compared based on their experiment (nic/smo) and direction of regulation (up/down); DEG were further compared against genes of DE exons and txs; mouse genes were also compared with human genes affected by cigarette smoke or associated with TUD. 4. Gene Ontology and KEGG: taking the DEG and the genes of DE txs and exons, GO & KEGG analyses were done and the expression levels of genes that participate in brain development related processes were explored. 5. DE feature visualization: DEG counts were represented in heatmaps in order to distinguish the groups of up and down-regulated genes. 6. Junction annotation: for novel DE jxns of unknown gene, their nearest, preceding and following genes were determined.

Abbreviations: Jxn: junction; Tx: transcript; CPM: counts per million; TPM: transcripts per million; TMM: Trimmed Mean of M-Values; TMMwsp: TMM with singleton pairing; EDA: exploratory data analysis; QC: quality control; ribo: ribosomal; mt: mitochondrial; PCA: Principal Component Analysis; PC: principal component; MDS: Multidimensional Scaling; DEA: differential expression analysis; DE: differential expression/differentially expressed; DEG: differentially expressed genes; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; TUD: tobacco use disorder.

1.3 Study design

Figure 1: Experimental design of the study. A) 36 pregnant dams and 35 non-pregnant female adult mice were either administered nicotine by intraperitoneal injection (IP; n=12), exposed to cigarette smoke in smoking chambers (n=24), or controls (n=35; 11 nicotine controls and 24 smoking controls). A total of 137 pups were born to pregnant dams: 19 were born to mice that were administered nicotine, 46 to mice exposed to cigarette smoke and the remaining 72 to control mice (23 to nicotine controls and 49 to smoking controls). Samples from frontal cortices of P0 pups and adults were obtained, as well as blood samples from smoking-exposed and smoking control adults. B) RNA was extracted, RNA-seq libraries were prepared and sequenced to obtain expression counts for genes, exons, transcripts and exon-exon junctions.

2 Basics

2.1 Install smokingMouse

R is an open-source statistical environment which can be easily modified to enhance its functionality via packages. smokingMouse is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can install smokingMouse by using the following commands in your R session:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("smokingMouse")

## Check that you have a valid Bioconductor installation
BiocManager::valid()

2.2 Required knowledge

smokingMouse is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with RNA-seq data and differential expression. That is, packages like SummarizedExperiment and limma.

If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.

2.3 Asking for help

As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But R and Bioconductor have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the smokingMouse tag and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.

2.4 Citing smokingMouse

We hope that smokingMouse will be useful for your research. Please use the following information to cite the package and the overall approach.

## Citation info
citation("smokingMouse")
#> To cite package 'smokingMouse' in publications use:
#> 
#>   Gonzalez-Padilla D, Collado-Torres L (2024). _Provides access to
#>   smokingMouse project data_. doi:10.18129/B9.bioc.smokingMouse
#>   <https://doi.org/10.18129/B9.bioc.smokingMouse>,
#>   https://github.com/LieberInstitute/smokingMouse/smokingMouse - R
#>   package version 1.4.0,
#>   <http://www.bioconductor.org/packages/smokingMouse>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Provides access to smokingMouse project data},
#>     author = {Daianna Gonzalez-Padilla and Leonardo Collado-Torres},
#>     year = {2024},
#>     url = {http://www.bioconductor.org/packages/smokingMouse},
#>     note = {https://github.com/LieberInstitute/smokingMouse/smokingMouse - R package version 1.4.0},
#>     doi = {10.18129/B9.bioc.smokingMouse},
#>   }

3 Quick start to using smokingMouse

To get started, please load the smokingMouse package.

library("smokingMouse")

4 smoking Mouse datasets

The raw data was generated by LIBD researchers and is composed of expression counts of genes, transcripts (txs), exons and exon-exon junctions (jxns) across 208 mice samples (brain/blood; adult/pup; nicotine-exposed/smoking-exposed/controls). The datasets available in smokingMouse were generated by Daianna Gonzalez-Padilla. The human data was generated by Semick, S.A. et al. (2018) in Mol Psychiatry, DOI: https://doi.org/10.1038/s41380-018-0223-1 and it contains the results of a DEA in adult and prenatal human brain samples exposed to cigarette smoke.

4.1 Description of the datasets

4.1.1 Mouse datasets:

  • They are 4 RangedSummarizedExperiment (RSE) objects that contain feature info in rowData(RSE) and sample info in colData(RSE).
  • Raw expression counts can be accessed with assays(RSE)$counts and the lognorm counts (log2(cpm + 0.5) for genes, exons and jxns; log2(tpm + 0.5) for txs) with assays(RSE)$logcounts.

4.1.2 Human datasets:

  • They are two data frames with the information of human genes and some relevant statistical metrics of differential expression (DE).

4.2 Data specifics

  • ‘rse_gene_mouse_RNAseq_nic-smo.Rdata’: (rse_gene object) the gene RSE object contains raw and normalized expression data of 55401 mouse genes across 208 samples from brains and blood of healthy and nicotine/smoking-exposed pup and adult mice.
  • ‘rse_tx_mouse_RNAseq_nic-smo.Rdata’: (rse_tx object) the tx RSE object contains raw and normalized expression data of 142604 mouse transcripts across 208 samples from brains and blood of healthy and nicotine/smoking-exposed pup and adult mice.
  • ‘rse_exon_mouse_RNAseq_nic-smo.Rdata’: (rse_exon object) the exon RSE object contains raw and normalized expression data of 447670 mouse exons across 208 samples from brains and blood of healthy and nicotine/smoking-exposed pup and adult mice.
  • ‘rse_jx_mouse_RNAseq_nic-smo.Rdata’: (rse_jx object) the jx RSE object contains raw and normalized expression data of 1436068 mouse exon-exon junctions across 208 samples from brains and blood of healthy and nicotine/smoking-exposed pup and adult mice.

All the above datasets contain sample and feature information and additional data of the results obtained in the filtering steps and the DEA.

  • ‘de_genes_prenatal_human_brain_smoking.Rdata’: (object with the same name) data frame with DE (ctrls vs smoking-exposed samples) data of 18067 genes in human prenatal brain samples exposed to cigarette smoke.
  • ‘de_genes_adult_human_brain_smoking.Rdata’: (object with the same name) data frame with DE (ctrls vs smoking-exposed samples) data of 18067 genes in human adult brain samples exposed to cigarette smoke.

4.3 Variables of mice data

Feature information in rowData(RSE) contains the following variables:

  • retained_after_feature_filtering: Boolean variable that equals TRUE if the feature passed the feature filtering based on expression levels and FALSE if not. Check code in here.
  • DE_in_adult_brain_nicotine: Boolean variable that equals TRUE if the feature is differentially expressed (DE) in adult brain samples exposed to nicotine and FALSE if not. Check code in here.
  • DE_in_adult_brain_smoking: Boolean variable that equals TRUE if the feature is differentially expressed (DE) in adult brain samples exposed to cigarette smoke and FALSE if not. Check code in here.
  • DE_in_adult_blood_smoking: Boolean variable that equals TRUE if the feature is differentially expressed (DE) in adult blood samples exposed to cigarette smoke and FALSE if not. Check code in here.
  • DE_in_pup_brain_nicotine: Boolean variable that equals TRUE if the feature is differentially expressed (DE) in pup brain samples exposed to nicotine and FALSE if not. Check code in here.
  • DE_in_pup_brain_smoking: Boolean variable that equals TRUE if the feature is differentially expressed (DE) in pup brain samples exposed to cigarette smoke and FALSE if not. Check code in here. The rest of the variables are outputs of SPEAQeasy pipeline. See here for a description of them.

Sample information in colData(RSE) contains the following variables:

  • The Quality Control (QC) variables sum,detected,subsets_Mito_sum, subsets_Mito_detected, subsets_Mito_percent, subsets_Ribo_sum,subsets_Ribo_detected and subsets_Ribo_percent are returned by addPerCellQC(). See here for more info.
  • retained_after_QC_sample_filtering: Boolean variable that equals TRUE if the sample passed the sample filtering based on QC metrics and FALSE if not. Check code in here.
  • retained_after_manual_sample_filtering: Boolean variable that equals TRUE if the sample passed the manual sample filtering based on PCA plots and FALSE if not. Check code in here The rest of the variables are outputs of SPEAQeasy. See here for their description.

4.4 Variables of human data

Check here to see the data generation and variables meaning.

4.5 Downloading the data with smokingMouse

Using smokingMouse you can download these R objects. They are hosted by Bioconductor’s ExperimentHub (Morgan and Shepherd, 2024) resource. Below you can see how to obtain these objects.

## Load ExperimentHub for downloading the data
library("ExperimentHub")
#> Loading required package: BiocGenerics
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: AnnotationHub
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr

## Connect to ExperimentHub
ehub <- ExperimentHub::ExperimentHub()

## Load the datasets of the package
myfiles <- query(ehub, "smokingMouse")

## Resulting smokingMouse files from our ExperimentHub query
myfiles
#> ExperimentHub with 6 records
#> # snapshotDate(): 2024-10-24
#> # $dataprovider: Lieber Institute for Brain Development (LIBD)
#> # $species: Mus musculus, Homo sapiens
#> # $rdataclass: RangedSummarizedExperiment, GenomicRanges
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["EH8313"]]' 
#> 
#>            title                                
#>   EH8313 | rse_gene_mouse_RNAseq_nic-smo        
#>   EH8314 | rse_tx_mouse_RNAseq_nic-smo          
#>   EH8315 | rse_jx_mouse_RNAseq_nic-smo          
#>   EH8316 | rse_exon_mouse_RNAseq_nic-smo        
#>   EH8317 | de_genes_prenatal_human_brain_smoking
#>   EH8318 | de_genes_adult_human_brain_smoking
## Load SummarizedExperiment which defines the class container for the data
library("SummarizedExperiment")
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: 'MatrixGenerics'
#> The following objects are masked from 'package:matrixStats':
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: 'Biobase'
#> The following object is masked from 'package:MatrixGenerics':
#> 
#>     rowMedians
#> The following objects are masked from 'package:matrixStats':
#> 
#>     anyMissing, rowMedians
#> The following object is masked from 'package:ExperimentHub':
#> 
#>     cache
#> The following object is masked from 'package:AnnotationHub':
#> 
#>     cache

######################
#     Mouse data 
######################
myfiles["EH8313"]
#> ExperimentHub with 1 record
#> # snapshotDate(): 2024-10-24
#> # names(): EH8313
#> # package(): smokingMouse
#> # $dataprovider: Lieber Institute for Brain Development (LIBD)
#> # $species: Mus musculus
#> # $rdataclass: RangedSummarizedExperiment
#> # $rdatadateadded: 2023-07-21
#> # $title: rse_gene_mouse_RNAseq_nic-smo
#> # $description: RangedSummarizedExperiment of bulk RNA-seq data from mouse b...
#> # $taxonomyid: 10090
#> # $genome: GRCm38
#> # $sourcetype: GTF
#> # $sourceurl: https://bioconductor.org/packages/smokingMouse
#> # $sourcesize: NA
#> # $tags: c("ExpressionData", "LIBD", "mouse", "Mus_musculus_Data",
#> #   "nicotine", "RNASeqData", "smoking") 
#> # retrieve record with 'object[["EH8313"]]'

## Download the mouse gene data
#  EH8313 | rse_gene_mouse_RNAseq_nic-smo
rse_gene <- myfiles[["EH8313"]]
#> see ?smokingMouse and browseVignettes('smokingMouse') for documentation
#> loading from cache

## This is a RangedSummarizedExperiment object
rse_gene
#> class: RangedSummarizedExperiment 
#> dim: 55401 208 
#> metadata(1): Obtained_from
#> assays(2): counts logcounts
#> rownames(55401): ENSMUSG00000102693.1 ENSMUSG00000064842.1 ...
#>   ENSMUSG00000064371.1 ENSMUSG00000064372.1
#> rowData names(13): Length gencodeID ... DE_in_pup_brain_nicotine
#>   DE_in_pup_brain_smoking
#> colnames: NULL
#> colData names(71): SAMPLE_ID FQCbasicStats ...
#>   retained_after_QC_sample_filtering
#>   retained_after_manual_sample_filtering

## Optionally check the memory size
# lobstr::obj_size(rse_gene)
# 159.68 MB

## Check sample info 
head(colData(rse_gene), 3)
#> DataFrame with 3 rows and 71 columns
#>     SAMPLE_ID FQCbasicStats perBaseQual perTileQual  perSeqQual perBaseContent
#>   <character>   <character> <character> <character> <character>    <character>
#> 1 Sample_2914          PASS        PASS        PASS        PASS      FAIL/WARN
#> 2 Sample_4042          PASS        PASS        PASS        PASS      FAIL/WARN
#> 3 Sample_4043          PASS        PASS        PASS        PASS      FAIL/WARN
#>     GCcontent    Ncontent SeqLengthDist SeqDuplication OverrepSeqs
#>   <character> <character>   <character>    <character> <character>
#> 1        WARN        PASS          WARN           FAIL        PASS
#> 2        WARN        PASS          WARN           FAIL        PASS
#> 3        WARN        PASS          WARN           FAIL        PASS
#>   AdapterContent KmerContent SeqLength_R1 percentGC_R1 phred15-19_R1
#>      <character> <character>  <character>  <character>   <character>
#> 1           PASS          NA       75-151           49          37.0
#> 2           PASS          NA       75-151           48          37.0
#> 3           PASS          NA       75-151           49          37.0
#>   phred65-69_R1 phred115-119_R1 phred150-151_R1 phredGT30_R1 phredGT35_R1
#>     <character>     <character>     <character>    <numeric>    <numeric>
#> 1          37.0            37.0            37.0           NA           NA
#> 2          37.0            37.0            37.0           NA           NA
#> 3          37.0            37.0            37.0           NA           NA
#>   Adapter65-69_R1 Adapter100-104_R1 Adapter140_R1 SeqLength_R2 percentGC_R2
#>         <numeric>         <numeric>     <numeric>  <character>  <character>
#> 1     0.000108294       0.000260890    0.00174971       75-151           49
#> 2     0.000210067       0.000352780    0.00154716       75-151           48
#> 3     0.000134434       0.000284284    0.00191475       75-151           49
#>   phred15-19_R2 phred65-69_R2 phred115-119_R2 phred150-151_R2 phredGT30_R2
#>     <character>   <character>     <character>     <character>    <numeric>
#> 1          37.0          37.0            37.0            37.0           NA
#> 2          37.0          37.0            37.0            37.0           NA
#> 3          37.0          37.0            37.0            37.0           NA
#>   phredGT35_R2 Adapter65-69_R2 Adapter100-104_R2 Adapter140_R2 ERCCsumLogErr
#>      <numeric>       <numeric>         <numeric>     <numeric>     <numeric>
#> 1           NA     0.000276104       0.000486875    0.00132235      -58.2056
#> 2           NA     0.000326771       0.000574851    0.00137044      -81.6359
#> 3           NA     0.000330534       0.000521084    0.00153550      -99.5348
#>                  bamFile   trimmed  numReads numMapped numUnmapped
#>              <character> <logical> <numeric> <numeric>   <numeric>
#> 1 Sample_2914_sorted.bam     FALSE  89386472  87621022     1765450
#> 2 Sample_4042_sorted.bam     FALSE  59980794  58967812     1012982
#> 3 Sample_4043_sorted.bam     FALSE  64864732  63961359      903373
#>   overallMapRate concordMapRate totalMapped mitoMapped  mitoRate
#>        <numeric>      <numeric>   <numeric>  <numeric> <numeric>
#> 1         0.9802         0.9748    87143087   10039739  0.103308
#> 2         0.9831         0.9709    58215746    7453208  0.113497
#> 3         0.9861         0.9811    62983384    8307331  0.116528
#>   totalAssignedGene  rRNA_rate      Tissue         Age         Sex        Expt
#>           <numeric>  <numeric> <character> <character> <character> <character>
#> 1          0.761378 0.00396315       Brain       Adult           F    Nicotine
#> 2          0.754444 0.00301119       Brain       Adult           F    Nicotine
#> 3          0.757560 0.00288706       Brain       Adult           F    Nicotine
#>          Group    Pregnant       plate    location concentration      medium
#>    <character> <character> <character> <character>   <character> <character>
#> 1 Experimental           0      Plate2         C12         165.9       Water
#> 2      Control           0      Plate1          B4         122.6       Water
#> 3      Control           0      Plate2          C9         128.5       Water
#>          date   Pregnancy    flowcell       sum  detected subsets_Mito_sum
#>   <character> <character> <character> <numeric> <numeric>        <numeric>
#> 1          NA          No   HKCMHDSXX  37119948     24435          2649559
#> 2          NA          No   HKCG7DSXX  24904754     23656          1913803
#> 3          NA          No   HKCMHDSXX  27083602     23903          2180712
#>   subsets_Mito_detected subsets_Mito_percent subsets_Ribo_sum
#>               <numeric>            <numeric>        <numeric>
#> 1                    26              7.13783           486678
#> 2                    31              7.68449           319445
#> 3                    31              8.05178           338277
#>   subsets_Ribo_detected subsets_Ribo_percent retained_after_QC_sample_filtering
#>               <numeric>            <numeric>                          <logical>
#> 1                    11              1.31110                               TRUE
#> 2                    13              1.28267                               TRUE
#> 3                    14              1.24901                               TRUE
#>   retained_after_manual_sample_filtering
#>                                <logical>
#> 1                                   TRUE
#> 2                                   TRUE
#> 3                                   TRUE

## Check gene info
head(rowData(rse_gene), 3)
#> DataFrame with 3 rows and 13 columns
#>                         Length            gencodeID          ensemblID
#>                      <integer>          <character>        <character>
#> ENSMUSG00000102693.1      1070 ENSMUSG00000102693.1 ENSMUSG00000102693
#> ENSMUSG00000064842.1       110 ENSMUSG00000064842.1 ENSMUSG00000064842
#> ENSMUSG00000051951.5      6094 ENSMUSG00000051951.5 ENSMUSG00000051951
#>                           gene_type    EntrezID          Symbol meanExprs
#>                         <character> <character>     <character> <numeric>
#> ENSMUSG00000102693.1            TEC       71042 MGI:MGI:1918292   0.00000
#> ENSMUSG00000064842.1          snRNA          NA              NA   0.00000
#> ENSMUSG00000051951.5 protein_coding      497097 MGI:MGI:3528744   7.94438
#>                      retained_after_feature_filtering DE_in_adult_blood_smoking
#>                                             <logical>                 <logical>
#> ENSMUSG00000102693.1                            FALSE                     FALSE
#> ENSMUSG00000064842.1                            FALSE                     FALSE
#> ENSMUSG00000051951.5                             TRUE                     FALSE
#>                      DE_in_adult_brain_nicotine DE_in_adult_brain_smoking
#>                                       <logical>                 <logical>
#> ENSMUSG00000102693.1                      FALSE                     FALSE
#> ENSMUSG00000064842.1                      FALSE                     FALSE
#> ENSMUSG00000051951.5                      FALSE                     FALSE
#>                      DE_in_pup_brain_nicotine DE_in_pup_brain_smoking
#>                                     <logical>               <logical>
#> ENSMUSG00000102693.1                    FALSE                   FALSE
#> ENSMUSG00000064842.1                    FALSE                   FALSE
#> ENSMUSG00000051951.5                    FALSE                   FALSE

## Access the original counts
class(assays(rse_gene)$counts)
#> [1] "matrix" "array"

## Access the log normalized counts
class(assays(rse_gene)$logcounts)
#> [1] "matrix" "array"
dim(assays(rse_gene)$logcounts)
#> [1] 55401   208
assays(rse_gene)$logcounts[1:3, 1:3]
#>                           [,1]      [,2]      [,3]
#> ENSMUSG00000102693.1 -5.985331 -5.985331 -5.985331
#> ENSMUSG00000064842.1 -5.985331 -5.985331 -5.985331
#> ENSMUSG00000051951.5  4.509114  4.865612  4.944597


######################
#     Human data 
######################
myfiles["EH8318"]
#> ExperimentHub with 1 record
#> # snapshotDate(): 2024-10-24
#> # names(): EH8318
#> # package(): smokingMouse
#> # $dataprovider: Lieber Institute for Brain Development (LIBD)
#> # $species: Homo sapiens
#> # $rdataclass: GenomicRanges
#> # $rdatadateadded: 2023-07-21
#> # $title: de_genes_adult_human_brain_smoking
#> # $description: GRanges with the information of the differentialy expressed ...
#> # $taxonomyid: 9606
#> # $genome: GRCh37
#> # $sourcetype: GTF
#> # $sourceurl: https://bioconductor.org/packages/smokingMouse
#> # $sourcesize: NA
#> # $tags: c("ExpressionData", "LIBD", "mouse", "Mus_musculus_Data",
#> #   "nicotine", "RNASeqData", "smoking") 
#> # retrieve record with 'object[["EH8318"]]'

## Download the human gene data
# EH8318 | de_genes_adult_human_brain_smoking
de_genes_prenatal_human_brain_smoking <- myfiles[["EH8318"]]
#> see ?smokingMouse and browseVignettes('smokingMouse') for documentation
#> loading from cache

## This is a GRanges object
class(de_genes_prenatal_human_brain_smoking)
#> [1] "GRanges"
#> attr(,"package")
#> [1] "GenomicRanges"
de_genes_prenatal_human_brain_smoking
#> GRanges object with 18067 ranges and 9 metadata columns:
#>                   seqnames              ranges strand |    Length      Symbol
#>                      <Rle>           <IRanges>  <Rle> | <integer> <character>
#>   ENSG00000019169     chr2 119699742-119752236      + |      2079       MARCO
#>   ENSG00000260400    chr10   70458257-70460551      + |      2295            
#>   ENSG00000011201     chrX     8496915-8700227      - |      7131        KAL1
#>   ENSG00000068438     chrX   48334541-48344752      + |      2740       FTSJ1
#>   ENSG00000151229    chr12   40148823-40499891      - |     10027     SLC2A13
#>               ...      ...                 ...    ... .       ...         ...
#>   ENSG00000141556    chr17   80709940-80900724      + |     10472        TBCD
#>   ENSG00000125804    chr20   26035291-26073683      + |      6332     FAM182A
#>   ENSG00000228998    chr15   90818266-90820841      + |      2576            
#>   ENSG00000149636    chr20   35380194-35402221      - |      2739        DSN1
#>   ENSG00000122644     chr7   12726481-12730559      + |      3561       ARL4A
#>                    EntrezID        logFC   AveExpr            t     P.Value
#>                   <integer>    <numeric> <numeric>    <numeric>   <numeric>
#>   ENSG00000019169      8685   -1.6032766  -1.80183     -6.14514 4.66989e-09
#>   ENSG00000260400      <NA>    0.1515813   1.17142      4.09836 6.18298e-05
#>   ENSG00000011201      3730    0.1423143   4.24576      4.09392 6.29277e-05
#>   ENSG00000068438     24140   -0.0495086   4.30660     -4.05975 7.20166e-05
#>   ENSG00000151229    114134    0.0842742   7.02625      4.00115 9.05839e-05
#>               ...       ...          ...       ...          ...         ...
#>   ENSG00000141556 101929597 -9.07984e-06   6.16583 -4.49543e-04    0.999642
#>   ENSG00000125804    728882 -2.02864e-05   2.75543 -2.93079e-04    0.999766
#>   ENSG00000228998      <NA>  1.05697e-05   4.14580  2.50417e-04    0.999800
#>   ENSG00000149636     79980  2.46976e-06   2.96401  1.02959e-04    0.999918
#>   ENSG00000122644     10124  1.62178e-06   4.51605  4.83868e-05    0.999961
#>                     adj.P.Val         B
#>                     <numeric> <numeric>
#>   ENSG00000019169 0.000084371   3.65960
#>   ENSG00000260400 0.325280946   1.21448
#>   ENSG00000011201 0.325280946   1.55562
#>   ENSG00000068438 0.325280946   1.43237
#>   ENSG00000151229 0.327315930   1.15523
#>               ...         ...       ...
#>   ENSG00000141556    0.999863  -6.30298
#>   ENSG00000125804    0.999911  -5.80161
#>   ENSG00000228998    0.999911  -6.07834
#>   ENSG00000149636    0.999961  -5.84217
#>   ENSG00000122644    0.999961  -6.13228
#>   -------
#>   seqinfo: 25 sequences from an unspecified genome; no seqlengths

## Optionally check the memory size
# lobstr::obj_size(de_genes_prenatal_human_brain_smoking)
# 3.73 MB

## Access data of human genes as normally do with other GenomicRanges::GRanges()
## objects or re-cast it as a data.frame
de_genes_df <- as.data.frame(de_genes_prenatal_human_brain_smoking)
head(de_genes_df)
#>                 seqnames     start       end  width strand Length  Symbol
#> ENSG00000019169     chr2 119699742 119752236  52495      +   2079   MARCO
#> ENSG00000260400    chr10  70458257  70460551   2295      +   2295        
#> ENSG00000011201     chrX   8496915   8700227 203313      -   7131    KAL1
#> ENSG00000068438     chrX  48334541  48344752  10212      +   2740   FTSJ1
#> ENSG00000151229    chr12  40148823  40499891 351069      -  10027 SLC2A13
#> ENSG00000136319    chr14  20724717  20774153  49437      -   9705    TTC5
#>                 EntrezID       logFC   AveExpr         t      P.Value
#> ENSG00000019169     8685 -1.60327659 -1.801830 -6.145143 4.669893e-09
#> ENSG00000260400       NA  0.15158127  1.171418  4.098360 6.182984e-05
#> ENSG00000011201     3730  0.14231431  4.245759  4.093917 6.292772e-05
#> ENSG00000068438    24140 -0.04950860  4.306597 -4.059746 7.201659e-05
#> ENSG00000151229   114134  0.08427416  7.026246  4.001149 9.058392e-05
#> ENSG00000136319    91875 -0.09445164  3.683599 -3.931427 1.186235e-04
#>                    adj.P.Val        B
#> ENSG00000019169 8.437096e-05 3.659604
#> ENSG00000260400 3.252809e-01 1.214477
#> ENSG00000011201 3.252809e-01 1.555617
#> ENSG00000068438 3.252809e-01 1.432373
#> ENSG00000151229 3.273159e-01 1.155227
#> ENSG00000136319 3.497224e-01 1.000380

5 Reproducibility

The smokingMouse package and the smoking mouse project were made possible thanks to:

This package was developed using biocthis.

Date the vignette was generated.

#> [1] "2024-10-31 13:03:30 EDT"

Wallclock time spent generating the vignette.

#> Time difference of 17.058 secs

R session information.

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#>  os       Ubuntu 24.04.1 LTS
#>  system   x86_64, linux-gnu
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#>  language (EN)
#>  collate  C
#>  ctype    en_US.UTF-8
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#>  date     2024-10-31
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6 Bibliography

This vignette was generated using BiocStyle (Oleś, 2024) with knitr (Xie, 2024) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.28. 2024. URL: https://github.com/rstudio/rmarkdown.

[2] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.

[3] M. Morgan and L. Shepherd. ExperimentHub: Client to access ExperimentHub resources. R package version 2.14.0. 2024. DOI: 10.18129/B9.bioc.ExperimentHub. URL: https://bioconductor.org/packages/ExperimentHub.

[4] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.34.0. 2024. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.

[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2024. URL: https://www.R-project.org/.

[6] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.

[7] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.2. 2021. URL: https://CRAN.R-project.org/package=sessioninfo.

[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.48. 2024. URL: https://yihui.org/knitr/.