FeatureDb objects

Description

The FeatureDb class is a generic container for storing genomic locations of an arbitrary type of genomic features.

See ?TxDb for a container for storing transcript annotations.

See ?makeFeatureDbFromUCSC for a convenient way to make FeatureDb objects from BioMart online resources.

Methods

In the code snippets below, x is a FeatureDb object.

metadata(x): Return x's metadata in a data frame.

Author(s)

Marc Carlson

See Also

• The TxDb class for storing transcript annotations.

• makeFeatureDbFromUCSC for a convenient way to make a FeatureDb object from UCSC online resources.

• saveDb and loadDb for saving and loading the database content of a FeatureDb object.

• features for how to extract genomic features from a FeatureDb object.

Examples

fdb_file <- system.file("extdata", "FeatureDb.sqlite",
                        package="GenomicFeatures")
fdb <- loadDb(fdb_file)
fdb

Results

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> library(GenomicFeatures)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicFeatures/FeatureDb-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FeatureDb-class
> ### Title: FeatureDb objects
> ### Aliases: FeatureDb-class class:FeatureDb FeatureDb
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> fdb_file <- system.file("extdata", "FeatureDb.sqlite",
+                         package="GenomicFeatures")
> fdb <- loadDb(fdb_file)
> fdb
FeatureDb object:
| Db type: FeatureDb
| data_nrow: 862
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2010-10-28 16:19:14 -0700 (Thu, 28 Oct 2010)
| GenomicFeatures version at creation time: 1.3.3
| RSQLite version at creation time: 0.9-3
| DBSCHEMAVERSION: 1.0
| Data source: UCSC
| Genome: hg18
| UCSC Table: cytoBand
| package: GenomicFeatures

Please see: help('select') for usage information
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