Last updated: 2020-04-26
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library(BgeeDB)
library(here)Verify the list of available species in BgeeDB and the correspondent data types for each species.
head(listBgeeSpecies())
Querying Bgee to get release information...
Building URL to query species in Bgee release 14_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1)
Query to Bgee webservice successful! ID GENUS SPECIES_NAME COMMON_NAME AFFYMETRIX EST IN_SITU
1 6239 Caenorhabditis elegans nematode TRUE FALSE TRUE
2 7217 Drosophila ananassae FALSE FALSE FALSE
3 7227 Drosophila melanogaster fruit fly TRUE TRUE TRUE
4 7230 Drosophila mojavensis FALSE FALSE FALSE
5 7237 Drosophila pseudoobscura FALSE FALSE FALSE
6 7240 Drosophila simulans FALSE FALSE FALSE
RNA_SEQ
1 TRUE
2 TRUE
3 TRUE
4 TRUE
5 TRUE
6 TRUEYou can verify the list of releases available in BgeeDB by using the listBgeeRelease() function.
listBgeeRelease()Downloading release information from Bgee... release release.date FTP.URL
1 14.1 2020-02-27 ftp://ftp.bgee.org/bgee_v14_1/
2 14.0 2018-02-21 ftp://ftp.bgee.org/bgee_v14_0/
3 13.2 2016-07-06 ftp://ftp.bgee.org/bgee_v13_2/
TopAnat.URL
1 https://r.bgee.org/bgee14_1/
2 https://r.bgee.org/bgee14/
3 https://r.bgee.org/bgee13/If you are interested in a particular release you can specify that by using the argument release and you are also able to order the table by a specific column, by speficying that in the argument order.
head(listBgeeSpecies(release = "13.2", order = 2))
Querying Bgee to get release information...
Building URL to query species in Bgee release 13_2...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee13/?page=species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1)
Query to Bgee webservice successful! ID GENUS SPECIES_NAME COMMON_NAME AFFYMETRIX EST IN_SITU
17 28377 Anolis carolinensis anolis FALSE FALSE FALSE
13 9913 Bos taurus cow FALSE FALSE FALSE
1 6239 Caenorhabditis elegans c.elegans TRUE FALSE TRUE
3 7955 Danio rerio zebrafish TRUE TRUE TRUE
2 7227 Drosophila melanogaster fruitfly TRUE TRUE TRUE
5 9031 Gallus gallus chicken FALSE FALSE FALSE
RNA_SEQ
17 TRUE
13 TRUE
1 TRUE
3 FALSE
2 FALSE
5 TRUEIn order to retrieve the annotations about the species and the data type of interest you have to create a Bgee object. In the species argument, you need to provide the name of the species or the NCBI taxonomic IDs.
For this part of the course we will use the Drosophila melanogaster data and the last release of Bgee (14.1).
DrosMelRNASeq <- Bgee$new(species = "Drosophila_melanogaster", dataType = "rna_seq")
Querying Bgee to get release information...
Building URL to query species in Bgee release 14_1...
Submitting URL to Bgee webservice... (https://r.bgee.org/bgee14_1/?page=r_package&action=get_all_species&display_type=tsv&source=BgeeDB_R_package&source_version=2.12.1)
Query to Bgee webservice successful!
API key built: 342617eeb6e728567eeaf07855efc4fa274e6ad21dde329ecce7bd3668c4efa9f23c364808e45b7b772594a592dfe6855ff75027e7983a848ff43a25416ebe6fannotation_DrosMelRNASeq <- getAnnotation(DrosMelRNASeq)
Saved annotation files in /Users/sfonseca1/Bgee/Drosophila_melanogaster_Bgee_14_1 folder.The output folder from the download should be saved in your current directory, where you should have a folder called: SPECIES_Bgee_release (in this particular case: Drosophila_melanogaster_Bgee_14_1).
From the information files (in this case: Drosophila_melanogaster_RNA-Seq_experiments.tsv or Drosophila_melanogaster_RNA-Seq_libraries.tsv) you are able to target experiments or libraries of interest before you start downloading the data.
Suggestion: Try to extract an experiment that have a minimum amount of 10 libraries and maximum of a 25 libraries in Drosophila melanogaster information file. During the filtering process allow the experiment to have samples in different conditions and samples in different stages.
annExperiments <- read.table(file = here("Drosophila_melanogaster_Bgee_14_1","Drosophila_melanogaster_RNA-Seq_experiments.tsv"), header=T, sep="\t")
experimentsId <- subset(annExperiments, Library.count > 10 & Library.count < 25 & Condition.count > 5 & Condition.count < 15 & Organ.stage.count > 5)
## retrieve experiments
unique(experimentsId) Experiment.ID
3 SRP002072
Experiment.name
3 Developmental Profile of the Drosophila Transcriptome by Paired-End RNA-Sequencing
Library.count Condition.count Organ.stage.count Organ.count Stage.count
3 12 10 9 4 9
Sex.count Strain.count Data.source Data.source.URL
3 2 0 SRA http://www.ncbi.nlm.nih.gov/sra/SRP002072
Bgee.normalized.data.URL
3 ftp://ftp.bgee.org/bgee_v14_1/download/processed_expr_values/rna_seq/Drosophila_melanogaster/Drosophila_melanogaster_RNA-Seq_read_counts_TPM_FPKM_SRP002072.tsv.tar.gz
Experiment.description
3 In order to gain a broad sampling of the Drosophila transcriptome, RNA-Seq experiments were performed at all stages of the Drosophila life cycle, and 12 independent cDNA libraries were generated, including embryonic, larval, pupal, and adult. Some libraries were staged as specific windows: 2-4 hour embryo, 14-16 hour embryo, 3rd instar larva, 3-day pupa, and 17-day adult. Additional libraries were derived from broadly staged mixed samples: embryo, larvae, and pupa. Three-day old male and female adults were sequenced separately for discovery of sex-specific variation. Finally, one library of mixed-age pupal RNA was sequenced in replicate as a validation of the technology. A total of 272 million paired-end reads of 64-75 base pairs in length were obtained, representing greater than 690x sequence coverage of the 30Mb Drosophila melanogaster transcriptome.
sessionInfo()R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] here_0.1 BgeeDB_2.12.1 tidyr_1.0.2
[4] topGO_2.38.1 SparseM_1.78 GO.db_3.10.0
[7] AnnotationDbi_1.48.0 IRanges_2.20.2 S4Vectors_0.24.4
[10] Biobase_2.46.0 graph_1.64.0 BiocGenerics_0.32.0
[13] workflowr_1.6.1
loaded via a namespace (and not attached):
[1] tidyselect_1.0.0 xfun_0.13 purrr_0.3.3 lattice_0.20-41
[5] vctrs_0.2.4 htmltools_0.4.0 yaml_2.2.1 blob_1.2.1
[9] rlang_0.4.5 later_1.0.0 pillar_1.4.3 glue_1.4.0
[13] DBI_1.1.0 bit64_0.9-7 matrixStats_0.56.0 lifecycle_0.2.0
[17] stringr_1.4.0 memoise_1.1.0 evaluate_0.14 knitr_1.28
[21] httpuv_1.5.2 fansi_0.4.1 Rcpp_1.0.4.6 promises_1.1.0
[25] backports_1.1.6 fs_1.4.1 bit_1.1-15.2 digest_0.6.25
[29] stringi_1.4.6 dplyr_0.8.5 rprojroot_1.3-2 grid_3.6.0
[33] cli_2.0.2 tools_3.6.0 bitops_1.0-6 magrittr_1.5
[37] RCurl_1.98-1.1 RSQLite_2.2.0 tibble_3.0.0 crayon_1.3.4
[41] whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.0 data.table_1.12.8
[45] assertthat_0.2.1 rmarkdown_2.1 R6_2.4.1 git2r_0.26.1
[49] compiler_3.6.0