Last updated: 2020-04-26
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If you do not want to use filters, as showed in the previous section (Extract Information) where you target a particular experiment to download, you can always download all the data of reference species using the getData() function. Note that in the getData() you should specify which data type you would like to retrieve from Bgee by specifying that in the argument dataType.
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: 342617eeb6e728567eeaf07855efc4fa274e6ad21dde329ecce7bd3668c4efa9f23c364808e45b7b772594a592dfe6855ff75027e7983a848ff43a25416ebe6fdataBgee_DM <- getData(DrosMelRNASeq)The experiment is not defined. Hence taking all rna_seq experiments available for Drosophila_melanogaster.Downloading expression data...Saved expression data file in/Users/sfonseca1/Bgee/Drosophila_melanogaster_Bgee_14_1 folder. Now untar file...Finished uncompress tar filesSaving all data in .rds file...## Number of experiments that exist in BgeeDB
length(dataBgee_DM)[1] 11In case you are interested in downloading a particular experiment (as showed before), anatomical entity or developmental stage, you can just download this data by specifying that in the respective arguments: experimentId , anatEntityId and stageId.
Taking your experimentId result from the filtering in previously section, download just this respective experiment by specifying that in the argument experimentId in the getData() function.
DrosMelRNASeq_SRP002072 <- getData(DrosMelRNASeq, experimentId = "SRP002072")Downloading expression data for the experiment SRP002072...Saved expression data file in /Users/sfonseca1/Bgee/Drosophila_melanogaster_Bgee_14_1 folder. Now untar file...Finished uncompress tar filesSaving all data in .rds file...head(DrosMelRNASeq_SRP002072) Experiment.ID Library.ID Library.type Gene.ID Anatomical.entity.ID
1 SRP002072 SRX019645 paired FBgn0000003 UBERON:0000922
2 SRP002072 SRX019645 paired FBgn0000008 UBERON:0000922
3 SRP002072 SRX019645 paired FBgn0000014 UBERON:0000922
4 SRP002072 SRX019645 paired FBgn0000015 UBERON:0000922
5 SRP002072 SRX019645 paired FBgn0000017 UBERON:0000922
6 SRP002072 SRX019645 paired FBgn0000018 UBERON:0000922
Anatomical.entity.name Stage.ID Stage.name Sex
1 embryo FBdv:00005306 embryonic stage 4 (Drosophila) <NA>
2 embryo FBdv:00005306 embryonic stage 4 (Drosophila) <NA>
3 embryo FBdv:00005306 embryonic stage 4 (Drosophila) <NA>
4 embryo FBdv:00005306 embryonic stage 4 (Drosophila) <NA>
5 embryo FBdv:00005306 embryonic stage 4 (Drosophila) <NA>
6 embryo FBdv:00005306 embryonic stage 4 (Drosophila) <NA>
Strain Read.count TPM FPKM Detection.flag Detection.quality
1 NA 5071.0000 7931.226169 10518.520218 present high quality
2 NA 172.0002 5.951876 7.893474 present high quality
3 NA 16.0000 0.604627 0.801867 present high quality
4 NA 19.0000 0.793388 1.052205 present high quality
5 NA 841.1847 22.824416 30.270109 present high quality
6 NA 94.0000 9.765199 12.950765 present high quality
State.in.Bgee
1 Part of a call
2 Part of a call
3 Part of a call
4 Part of a call
5 Part of a call
6 Part of a callNote that in the next sub-sections the arguments anatEntityId and stageId in the getData() function are implemented just in BgeeDB package in the Bioconductor release 3.11.
You are also able to retrieve data from the database by specifying the anatomic entity of interest for this particular experiment. Here we will target adult organism as an example.
DrosMelRNASeq_annEnt <- getData(DrosMelRNASeq, experimentId = "SRP002072", anatEntityId = "UBERON:0007023")
head(DrosMelRNASeq_annEnt)Note you can specify more than one anatomical entity in the anatEntityId argument.
DrosMelRNASeq_annEnt_plus <- getData(DrosMelRNASeq, experimentId = "SRP002072", anatEntityId = c("UBERON:0007023","UBERON:0000922","UBERON:0002548"))
head(DrosMelRNASeq_annEnt_plus)As demonstrated before, for experiment and anatomical entities, you also can download data by specifying your target developmental stage of interest in the stageId argument.
DrosMelRNASeq_SRP002072_stg <- getData(DrosMelRNASeq, stageId = c("UBERON:0000068","FBdv:00005341"))
head(DrosMelRNASeq_SRP002072_stg)
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] BgeeDB_2.12.1 tidyr_1.0.2 topGO_2.38.1
[4] SparseM_1.78 GO.db_3.10.0 AnnotationDbi_1.48.0
[7] IRanges_2.20.2 S4Vectors_0.24.4 Biobase_2.46.0
[10] graph_1.64.0 BiocGenerics_0.32.0 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