Last updated: 2024-07-26
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Knit directory: muse/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e897914 | Dave Tang | 2024-07-26 | dbplyr basics |
| html | 47f20cf | Dave Tang | 2024-07-26 | Build site. |
| Rmd | a9be34e | Dave Tang | 2024-07-26 | Connect to SQLite and make some basic queries |
| html | 6917788 | Dave Tang | 2024-07-17 | Build site. |
| Rmd | bb8ad42 | Dave Tang | 2024-07-17 | Database basics |
The {DBI} package provides:
A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.
A database table can be thought of as a data frame, however there are three high-level differences between them:
Database tables are stored on disk and can be arbitrarily large, whereas data frames are stored in memory and are fundamentally limited.
Database tables almost always have indexes making it possible to quickly find rows of interest without having to look at every single row. Data frames don’t have indexes but data tables do, which is one of the reasons why they’re so fast.
Most classical databases are optimised for rapidly collecting data and not for analysing existing data. These databases are called row-oriented because the data is stored row by row, rather than column by column like data frames. More recently, there’s been much development of column-oriented databases that make analysing existing data much faster.
Databases are run by database management systems (DBMS), which come in three basic forms:
Client-server DBMS run on a powerful central server, which you connect from your computer (the client). They are useful for sharing data with multiple people and popular client-server DBMS include PostgreSQL, MariaDB, SQL Server, and Oracle.
Cloud DBMS, like Snowflake, Amazon’s RedShift, and Google’s BigQuery, are similar to client-server DBMS, but they run in the cloud, taking advantage of cloud capabilities.
In-process DBMS, like SQLite or duckdb, run entirely on your computer. They’re great for working with large datasets where you are the primary user.
To connect to a database in R, we need:
The {RSQLite} package provides a SQLite interface for R.
Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine and for various extensions in a recent version is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations.
SQLite database downloaded as per the post Interfacing with the Sequence Read Archive in R.
dbfile <- "/data2/sradb/SRAmetadb.sqlite"
mydb <- dbConnect(RSQLite::SQLite(), dbname = dbfile)
mydb<SQLiteConnection>
Path: /data2/sradb/SRAmetadb.sqlite
Extensions: TRUELists all tables in the database.
tabs <- dbListTables(mydb)
tabs [1] "col_desc" "experiment" "metaInfo" "run"
[5] "sample" "sra" "sra_ft" "sra_ft_content"
[9] "sra_ft_segdir" "sra_ft_segments" "study" "submission" Neat trick to get the fields of a table.
get_fields <- "SELECT * FROM run WHERE 1=0"
DBI::dbGetQuery(mydb, get_fields) [1] run_ID bamFile run_alias
[4] run_accession broker_name instrument_name
[7] run_date run_file run_center
[10] total_data_blocks experiment_accession experiment_name
[13] sra_link run_url_link xref_link
[16] run_entrez_link ddbj_link ena_link
[19] run_attribute submission_accession sradb_updated
<0 rows> (or 0-length row.names)Save all table fields.
table_fields <- purrr::map(tabs, \(x){
sql <- paste0('SELECT * FROM ', x, ' WHERE 1=0')
DBI::dbGetQuery(mydb, sql)
})
names(table_fields) <- tabs
table_fields[[1]][1] col_desc_ID table_name field_name type description
[6] value_list sradb_updated
<0 rows> (or 0-length row.names)table_fields$col_desc
[1] col_desc_ID table_name field_name type description
[6] value_list sradb_updated
<0 rows> (or 0-length row.names)
$experiment
[1] experiment_ID bamFile
[3] fastqFTP experiment_alias
[5] experiment_accession broker_name
[7] center_name title
[9] study_name study_accession
[11] design_description sample_name
[13] sample_accession sample_member
[15] library_name library_strategy
[17] library_source library_selection
[19] library_layout targeted_loci
[21] library_construction_protocol spot_length
[23] adapter_spec read_spec
[25] platform instrument_model
[27] platform_parameters sequence_space
[29] base_caller quality_scorer
[31] number_of_levels multiplier
[33] qtype sra_link
[35] experiment_url_link xref_link
[37] experiment_entrez_link ddbj_link
[39] ena_link experiment_attribute
[41] submission_accession sradb_updated
<0 rows> (or 0-length row.names)
$metaInfo
[1] name value
<0 rows> (or 0-length row.names)
$run
[1] run_ID bamFile run_alias
[4] run_accession broker_name instrument_name
[7] run_date run_file run_center
[10] total_data_blocks experiment_accession experiment_name
[13] sra_link run_url_link xref_link
[16] run_entrez_link ddbj_link ena_link
[19] run_attribute submission_accession sradb_updated
<0 rows> (or 0-length row.names)
$sample
[1] sample_ID sample_alias sample_accession
[4] broker_name center_name taxon_id
[7] scientific_name common_name anonymized_name
[10] individual_name description sra_link
[13] sample_url_link xref_link sample_entrez_link
[16] ddbj_link ena_link sample_attribute
[19] submission_accession sradb_updated
<0 rows> (or 0-length row.names)
$sra
[1] sra_ID SRR_bamFile
[3] SRX_bamFile SRX_fastqFTP
[5] run_ID run_alias
[7] run_accession run_date
[9] updated_date spots
[11] bases run_center
[13] experiment_name run_url_link
[15] run_entrez_link run_attribute
[17] experiment_ID experiment_alias
[19] experiment_accession experiment_title
[21] study_name sample_name
[23] design_description library_name
[25] library_strategy library_source
[27] library_selection library_layout
[29] library_construction_protocol adapter_spec
[31] read_spec platform
[33] instrument_model instrument_name
[35] platform_parameters sequence_space
[37] base_caller quality_scorer
[39] number_of_levels multiplier
[41] qtype experiment_url_link
[43] experiment_entrez_link experiment_attribute
[45] sample_ID sample_alias
[47] sample_accession taxon_id
[49] common_name anonymized_name
[51] individual_name description
[53] sample_url_link sample_entrez_link
[55] sample_attribute study_ID
[57] study_alias study_accession
[59] study_title study_type
[61] study_abstract center_project_name
[63] study_description study_url_link
[65] study_entrez_link study_attribute
[67] related_studies primary_study
[69] submission_ID submission_accession
[71] submission_comment submission_center
[73] submission_lab submission_date
[75] sradb_updated
<0 rows> (or 0-length row.names)
$sra_ft
[1] SRR_bamFile SRX_bamFile
[3] SRX_fastqFTP run_ID
[5] run_alias run_accession
[7] run_date updated_date
[9] spots bases
[11] run_center experiment_name
[13] run_url_link run_entrez_link
[15] run_attribute experiment_ID
[17] experiment_alias experiment_accession
[19] experiment_title study_name
[21] sample_name design_description
[23] library_name library_strategy
[25] library_source library_selection
[27] library_layout library_construction_protocol
[29] adapter_spec read_spec
[31] platform instrument_model
[33] instrument_name platform_parameters
[35] sequence_space base_caller
[37] quality_scorer number_of_levels
[39] multiplier qtype
[41] experiment_url_link experiment_entrez_link
[43] experiment_attribute sample_ID
[45] sample_alias sample_accession
[47] taxon_id common_name
[49] anonymized_name individual_name
[51] description sample_url_link
[53] sample_entrez_link sample_attribute
[55] study_ID study_alias
[57] study_accession study_title
[59] study_type study_abstract
[61] center_project_name study_description
[63] study_url_link study_entrez_link
[65] study_attribute related_studies
[67] primary_study submission_ID
[69] submission_accession submission_comment
[71] submission_center submission_lab
[73] submission_date sradb_updated
<0 rows> (or 0-length row.names)
$sra_ft_content
[1] docid c0SRR_bamFile
[3] c1SRX_bamFile c2SRX_fastqFTP
[5] c3run_ID c4run_alias
[7] c5run_accession c6run_date
[9] c7updated_date c8spots
[11] c9bases c10run_center
[13] c11experiment_name c12run_url_link
[15] c13run_entrez_link c14run_attribute
[17] c15experiment_ID c16experiment_alias
[19] c17experiment_accession c18experiment_title
[21] c19study_name c20sample_name
[23] c21design_description c22library_name
[25] c23library_strategy c24library_source
[27] c25library_selection c26library_layout
[29] c27library_construction_protocol c28adapter_spec
[31] c29read_spec c30platform
[33] c31instrument_model c32instrument_name
[35] c33platform_parameters c34sequence_space
[37] c35base_caller c36quality_scorer
[39] c37number_of_levels c38multiplier
[41] c39qtype c40experiment_url_link
[43] c41experiment_entrez_link c42experiment_attribute
[45] c43sample_ID c44sample_alias
[47] c45sample_accession c46taxon_id
[49] c47common_name c48anonymized_name
[51] c49individual_name c50description
[53] c51sample_url_link c52sample_entrez_link
[55] c53sample_attribute c54study_ID
[57] c55study_alias c56study_accession
[59] c57study_title c58study_type
[61] c59study_abstract c60center_project_name
[63] c61study_description c62study_url_link
[65] c63study_entrez_link c64study_attribute
[67] c65related_studies c66primary_study
[69] c67submission_ID c68submission_accession
[71] c69submission_comment c70submission_center
[73] c71submission_lab c72submission_date
[75] c73sradb_updated
<0 rows> (or 0-length row.names)
$sra_ft_segdir
[1] level idx start_block leaves_end_block
[5] end_block root
<0 rows> (or 0-length row.names)
$sra_ft_segments
[1] blockid block
<0 rows> (or 0-length row.names)
$study
[1] study_ID study_alias study_accession
[4] study_title study_type study_abstract
[7] broker_name center_name center_project_name
[10] study_description related_studies primary_study
[13] sra_link study_url_link xref_link
[16] study_entrez_link ddbj_link ena_link
[19] study_attribute submission_accession sradb_updated
<0 rows> (or 0-length row.names)
$submission
[1] submission_ID submission_alias submission_accession
[4] submission_comment files broker_name
[7] center_name lab_name submission_date
[10] sra_link submission_url_link xref_link
[13] submission_entrez_link ddbj_link ena_link
[16] submission_attribute sradb_updated
<0 rows> (or 0-length row.names)Use tbl() to create an object that represents a database
table.
run_db <- tbl(src = mydb, 'run')
run_db# Source: table<`run`> [?? x 21]
# Database: sqlite 3.46.0 [/data2/sradb/SRAmetadb.sqlite]
run_ID bamFile run_alias run_accession broker_name instrument_name run_date
<dbl> <chr> <chr> <chr> <chr> <chr> <chr>
1 1 <NA> 2008-09-12… DRR000001 <NA> <NA> 2008-09…
2 2 <NA> 2008-09-12… DRR000002 <NA> <NA> 2008-09…
3 3 <NA> DRR000004 DRR000004 <NA> <NA> 2009-03…
4 4 <NA> DRR000005 DRR000005 <NA> <NA> 2009-03…
5 5 <NA> DRR000006 DRR000006 <NA> <NA> 2009-03…
6 6 <NA> DRR000007 DRR000007 <NA> <NA> 2009-02…
7 7 <NA> DRR000363 DRR000363 <NA> <NA> 2010-02…
8 8 <NA> DRR000364 DRR000364 <NA> <NA> 2010-02…
9 9 <NA> DRR000365 DRR000365 <NA> <NA> 2010-02…
10 10 <NA> DRR000366 DRR000366 <NA> <NA> 2010-02…
# ℹ more rows
# ℹ 14 more variables: run_file <chr>, run_center <chr>,
# total_data_blocks <int>, experiment_accession <chr>, experiment_name <chr>,
# sra_link <chr>, run_url_link <chr>, xref_link <chr>, run_entrez_link <chr>,
# ddbj_link <chr>, ena_link <chr>, run_attribute <chr>,
# submission_accession <chr>, sradb_updated <chr>Select specific fields.
run_db |>
select(run_accession, experiment_name)# Source: SQL [?? x 2]
# Database: sqlite 3.46.0 [/data2/sradb/SRAmetadb.sqlite]
run_accession experiment_name
<chr> <chr>
1 DRR000001 DRX000001
2 DRR000002 DRX000002
3 DRR000004 DRX000003
4 DRR000005 DRX000003
5 DRR000006 DRX000003
6 DRR000007 DRX000003
7 DRR000363 DRX000003
8 DRR000364 DRX000003
9 DRR000365 DRX000003
10 DRR000366 DRX000003
# ℹ more rowsSRA table.
sra_db <- tbl(src = mydb, 'sra')
sra_db# Source: table<`sra`> [?? x 75]
# Database: sqlite 3.46.0 [/data2/sradb/SRAmetadb.sqlite]
sra_ID SRR_bamFile SRX_bamFile SRX_fastqFTP run_ID run_alias run_accession
<dbl> <chr> <chr> <chr> <dbl> <chr> <chr>
1 1 <NA> <NA> <NA> 1 2008-09-12.… DRR000001
2 2 <NA> <NA> <NA> 2 2008-09-12.… DRR000002
3 3 <NA> <NA> <NA> 11 DRR000003 DRR000003
4 4 <NA> <NA> <NA> 5 DRR000006 DRR000006
5 5 <NA> <NA> <NA> 3 DRR000004 DRR000004
6 6 <NA> <NA> <NA> 7 DRR000363 DRR000363
7 7 <NA> <NA> <NA> 6 DRR000007 DRR000007
8 8 <NA> <NA> <NA> 10 DRR000366 DRR000366
9 9 <NA> <NA> <NA> 4 DRR000005 DRR000005
10 10 <NA> <NA> <NA> 8 DRR000364 DRR000364
# ℹ more rows
# ℹ 68 more variables: run_date <chr>, updated_date <chr>, spots <dbl>,
# bases <dbl>, run_center <chr>, experiment_name <chr>, run_url_link <chr>,
# run_entrez_link <chr>, run_attribute <chr>, experiment_ID <dbl>,
# experiment_alias <chr>, experiment_accession <chr>, experiment_title <chr>,
# study_name <chr>, sample_name <chr>, design_description <chr>,
# library_name <chr>, library_strategy <chr>, library_source <chr>, …Disconnect.
DBI::dbDisconnect(mydb)
sessionInfo()R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[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
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[5] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[9] ggplot2_3.5.1 tidyverse_2.0.0 dbplyr_2.5.0 RSQLite_2.3.7
[13] DBI_1.2.3 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] sass_0.4.9 utf8_1.2.4 generics_0.1.3 stringi_1.8.4
[5] hms_1.1.3 digest_0.6.35 magrittr_2.0.3 timechange_0.3.0
[9] evaluate_0.24.0 grid_4.4.0 fastmap_1.2.0 blob_1.2.4
[13] rprojroot_2.0.4 jsonlite_1.8.8 processx_3.8.4 whisker_0.4.1
[17] ps_1.7.6 promises_1.3.0 httr_1.4.7 fansi_1.0.6
[21] scales_1.3.0 jquerylib_0.1.4 cli_3.6.2 rlang_1.1.4
[25] munsell_0.5.1 bit64_4.0.5 withr_3.0.0 cachem_1.1.0
[29] yaml_2.3.8 tools_4.4.0 tzdb_0.4.0 memoise_2.0.1
[33] colorspace_2.1-0 httpuv_1.6.15 vctrs_0.6.5 R6_2.5.1
[37] lifecycle_1.0.4 git2r_0.33.0 fs_1.6.4 bit_4.0.5
[41] pkgconfig_2.0.3 callr_3.7.6 gtable_0.3.5 pillar_1.9.0
[45] bslib_0.7.0 later_1.3.2 glue_1.7.0 Rcpp_1.0.12
[49] xfun_0.44 tidyselect_1.2.1 rstudioapi_0.16.0 knitr_1.47
[53] htmltools_0.5.8.1 rmarkdown_2.27 compiler_4.4.0 getPass_0.2-4