The MgDb Class in the metagenomeFeatures package includes the sequences and taxonomic information for a 16S database. The following vignette demonstrates the class methods for exploring and subsetting a MgDb-class object using the demoMgDb included in the metagenomeFeatures package. MgDb-class object with full databases are inseparte packages such as the greengenes13.5MgDb package.
MgDb-class Objectlibrary(metagenomeFeatures)
demoMgDb <- get_demoMgDb()
demoMgDb## MgDb object:[1] "Metadata"
## |ACCESSION_DATE: 3/31/2015
## |URL: https://greengenes.microbio.me
## |DB_TYPE_NAME: GreenGenes-MgDb-Demo
## |DB_TYPE_VALUE: MgDb
## |DB_SCHEMA_VERSION: 1.0
## [1] "Sequence Data:"
## A DNAStringSet instance of length 249
## width seq names
## [1] 1343 GACGAACGCTGGCGGCGTGC...TGAATACGTTCCCGGGCCT 1093016
## [2] 1326 GACGAACGCTGGCGGCGTGC...TGAATACGTTCCCGGGCCT 1083934
## [3] 1334 GATGAACGCTGGCGGCACGC...TGAATGCGTTCCCGGGCCT 1075456
## [4] 1345 GATGAACGCTAGCGGGAGGC...TGAATACGTTCCCGGGCCT 1023948
## [5] 1504 GACGAACGCTGGCGGCGCGC...GGGGTTGATGATTGGGGTG 983909
## ... ... ...
## [245] 1422 TCCGGTTGATCCTGCCGGAG...TCGAAACTGGGCCTCGCGA 4327819
## [246] 1419 CACTGCTATTGGAGTCCGAC...GGGGTTGCGTGAGGGGGGC 4344031
## [247] 1343 CGGTTGATCCTGCCGAAGGC...CCTTGCACACACCGCCCGT 4357608
## [248] 1270 TAACGTGAAGACCGGGATAA...CGAGCAGGTTTTAGGTGAG 4437875
## [249] 1554 TTTTTTCTGAGAATTTGATC...GGGCTGGATCACCTCCTTT 4485266
## [1] "Taxonomy Data:"
## Source: sqlite 3.8.6 [/tmp/RtmpjUAPWW/Rinst17802a100cbe/metagenomeFeatures/extdata/demoTaxa.sqlite]
## From: taxa [249 x 8]
##
## Keys Kingdom Phylum Class
## (chr) (chr) (chr) (chr)
## 1 4324716 k__Bacteria p__Bacteroidetes c__
## 2 246960 k__Bacteria p__Planctomycetes c__028H05-P-BN-P5
## 3 222675 k__Bacteria p__Armatimonadetes c__0319-6E2
## 4 156874 k__Bacteria p__NC10 c__12-24
## 5 4383832 k__Bacteria p__GN02 c__3BR-5F
## 6 4383502 k__Bacteria p__Elusimicrobia c__4-29
## 7 315344 k__Bacteria p__Cyanobacteria c__4C0d-2
## 8 2655590 k__Bacteria p__GN04 c__5bav_B12
## 9 552241 k__Bacteria p__SBR1093 c__A712011
## 10 4327819 k__Archaea p__Crenarchaeota c__AAG
## .. ... ... ... ...
## Variables not shown: Order (chr), Family (chr), Genus (chr), Species (chr)taxa_keytypes
taxa_keytypes(demoMgDb)## [1] "Keys" "Kingdom" "Phylum" "Class" "Order" "Family" "Genus"
## [8] "Species"taxa_columns(demoMgDb)## [1] "Keys" "Kingdom" "Phylum" "Class" "Order" "Family" "Genus"
## [8] "Species"head(taxa_keys(demoMgDb, keytype = c("Kingdom")))## Source: local data frame [6 x 1]
##
## Kingdom
## (chr)
## 1 k__Bacteria
## 2 k__Bacteria
## 3 k__Bacteria
## 4 k__Bacteria
## 5 k__Bacteria
## 6 k__BacteriaUsed to retrieve db entries for a specified taxanomic group or id list, can return either taxonomic, sequences information, or both.
select(demoMgDb, type = "taxa",
keys = c("Vibrio", "Salmonella"),
keytype = "Genus")## Source: local data frame [0 x 8]
##
## Variables not shown: Keys (chr), Kingdom (chr), Phylum (chr), Class (chr),
## Order (chr), Family (chr), Genus (chr), Species (chr)select(demoMgDb, type = "seq",
keys = c("Vibrio", "Salmonella"),
keytype = "Genus")## A DNAStringSet instance of length 0select(demoMgDb, type = "both",
keys = c("Vibrio", "Salmonella"),
keytype = "Genus")## $taxa
## Source: local data frame [0 x 8]
##
## Variables not shown: Keys (chr), Kingdom (chr), Phylum (chr), Class (chr),
## Order (chr), Family (chr), Genus (chr), Species (chr)
##
## $seq
## A DNAStringSet instance of length 0sessionInfo()## R Under development (unstable) (2015-09-09 r69333)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.3 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [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
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] Biostrings_2.39.0 XVector_0.11.0
## [3] IRanges_2.5.0 S4Vectors_0.9.0
## [5] metagenomeSeq_1.13.0 RColorBrewer_1.1-2
## [7] glmnet_2.0-2 foreach_1.4.3
## [9] Matrix_1.2-2 limma_3.27.0
## [11] metagenomeFeatures_1.1.0 Biobase_2.31.0
## [13] BiocGenerics_0.17.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.1 formatR_1.2.1
## [3] futile.logger_1.4.1 GenomeInfoDb_1.7.0
## [5] bitops_1.0-6 futile.options_1.0.0
## [7] iterators_1.0.8 tools_3.3.0
## [9] zlibbioc_1.17.0 digest_0.6.8
## [11] evaluate_0.8 RSQLite_1.0.0
## [13] lattice_0.20-33 DBI_0.3.1
## [15] yaml_2.1.13 dplyr_0.4.3
## [17] stringr_1.0.0 hwriter_1.3.2
## [19] knitr_1.11 caTools_1.17.1
## [21] gtools_3.5.0 grid_3.3.0
## [23] R6_2.1.1 BiocParallel_1.5.0
## [25] rmarkdown_0.8.1 gdata_2.17.0
## [27] latticeExtra_0.6-26 lambda.r_1.1.7
## [29] magrittr_1.5 gplots_2.17.0
## [31] matrixStats_0.14.2 Rsamtools_1.23.0
## [33] codetools_0.2-14 htmltools_0.2.6
## [35] GenomicRanges_1.23.0 GenomicAlignments_1.7.0
## [37] assertthat_0.1 ShortRead_1.29.0
## [39] SummarizedExperiment_1.1.0 KernSmooth_2.23-15
## [41] stringi_0.5-5 lazyeval_0.1.10