rtracklayer (version 1.32.0)

QuickloadGenome-class: Quickload Genome Access

Description

A Quickload data source is a collection of tracks and sequences, separated by genome. This class, QuickloadGenome provides direct access to the data for one particular genome.

Examples

tests_dir <- system.file("tests", package = "rtracklayer")
ql <- Quickload(file.path(tests_dir, "quickload"))
qlg <- QuickloadGenome(ql, "T_species_Oct_2011")
seqinfo(qlg)
organism(qlg)
releaseDate(qlg)
names(qlg)
mcols(qlg)
if (.Platform$OS.type != "windows") { # temporary
qlg$bedData
}

## populating the test repository
ql <- Quickload(file.path(tests_dir, "quickload"), create = TRUE)
reference_seq <- import(file.path(tests_dir, "test.2bit"))
names(reference_seq) <- "test"
qlg <- QuickloadGenome(ql, "T_species_Oct_2011", create = TRUE,
                       seqinfo = seqinfo(reference_seq))
referenceSequence(qlg) <- reference_seq
test_bed <- import(file.path(tests_dir, "test.bed"))
names(test_bed) <- "test"
qlg$bedData <- test_bed
test_bedGraph <- import(file.path(tests_dir, "test.bedGraph"))
names(test_bedGraph) <- "test"
start(test_bedGraph) <- seq(1, 90, 10)
width(test_bedGraph) <- 10
track(qlg, "bedGraphData", format = "bw") <- test_bedGraph