| Title: | Hub package for the precomputed data of CENTRE and example data |
|---|---|
| Description: | Interface and documentation for the Experiment Hub records needed by the CENTRE Bioconductor software package. The Experiment Hub records contains the precomputed fisher combined p-values, CRUP correlations. Additionally, the records hold ChIP-seq and RNA-seq data used for the example of the software package. |
| Authors: | Sara Lopez Ruiz de Vargas [aut, cre] (ORCID: <https://orcid.org/0000-0002-1290-4774>) |
| Maintainer: | Sara Lopez Ruiz de Vargas <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.2.0 |
| Built: | 2026-10-10 11:17:28 UTC |
| Source: | https://github.com/bioc/CENTREprecomputed |
The CENTREprecompDb object provides access to CENTRE's Precomputed SQLite
Database PrecomputedDataLight.db. Inside the database is combinedTestData,
crup_cor and metadata. For more information check the
computeGenericFeatures() function from the CENTRE package.
CENTREprecompDb(x) tables(x)CENTREprecompDb(x) tables(x)
x |
sqlite file path |
CENTREprecompDb is the object that provides access to CENTRE's database.
tables(CENTREprecompDb) shows the tables inside the database and
their columns.
Object of class CENTREprecompDb
Based on CompoundDb::CompDb class.
#The object is accessed through the ExperimentHub record eh <- ExperimentHub::ExperimentHub() centreprecompdb <- eh[["EH9540"]] tables(centreprecompdb)#The object is accessed through the ExperimentHub record eh <- ExperimentHub::ExperimentHub() centreprecompdb <- eh[["EH9540"]] tables(centreprecompdb)
Function to fetch data from the CENTREprecomputed package database
through the CENTREprecompDb object.
fetch_data_precomp(x, table, columns, entries, column_filter)fetch_data_precomp(x, table, columns, entries, column_filter)
x |
|
table |
Table of the database on which to search. Can be combinedTestData or cor_CRUP. |
columns |
Columns to select. Equivalent to X in SELECT X. |
entries |
Element ID to select. Equivalen to ID in SELECT X FROM TABLE WHERE ID in Z. If entries or column_filter is missing the program assumes the query is SELECT X FROM TABLE. |
column_filter |
Column on which to apply filter. Equivalent to Z in SELECT X FROM TABLE WHERE ID in Z. If entries or column_filter is missing the program assumes the query is SELECT X FROM TABLE. |
data.frame with the data queried.
Based on the package CompoundDb query engine internal functions.
vignette("CENTREprecomputed")
eh <- ExperimentHub::ExperimentHub() centreprecompdb <- eh[["EH9540"]] res <- fetch_data_precomp(centreprecompdb, table = "crup_cor", columns = c("pair", "cor_CRUP"), entries = "EH38E3440167", column_filter = "symbol38" )eh <- ExperimentHub::ExperimentHub() centreprecompdb <- eh[["EH9540"]] res <- fetch_data_precomp(centreprecompdb, table = "crup_cor", columns = c("pair", "cor_CRUP"), entries = "EH38E3440167", column_filter = "symbol38" )