biovizBase (version 1.20.0)

crunch: Fetching GRanges from various data source

Description

Fetching Granges from various data source, currently supported objects are TxDb, EnsDb, GAlignments and BamFile.

Usage

"crunch"(obj, which, columns = c("tx_id", "tx_name","gene_id"), type = c("all", "reduce"), truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025)
"crunch"(obj, which, columns = c("tx_id", "gene_name","gene_id"), type = c("all", "reduce"), truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025)
"crunch"(obj, which, truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025)
"crunch"(obj, which, ..., type = c("gapped.pair", "raw", "all"), truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025)

Arguments

obj

supported objects are TxDb, GAlignments and BamFile.

which

GRanges object. For TxDb object, could aslo be a list. For EnsDb, it can also be a single filter object extending BasicFilter-class or a list of such objects.

columns

columns to include in the output.

type

default 'all' is to show the full model, 'reduce' is to show a single model.

truncate.gaps

logical value, default FALSE. Whether to truncate gaps or not.

truncate.fun

shrinkage function.

ratio

numeric value, shrinking ratio.

...

arguments passed to function readGAlignments.

Value

GRanges object.

Examples

library(biovizBase)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
data(genesymbol, package = "biovizBase")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
obj <- txdb
temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "all")
temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "reduce")

## Fetching data from a EnsDb object.
library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75
gr <- genesymbol["BRCA1"]
seqlevels(gr) <- sub(seqlevels(gr), pattern="chr", replacement="")
temp <- crunch(edb, which=gr)

## Alternatively, use the GenenameFilter from the ensembldb package:
temp <- crunch(edb, which=GenenameFilter("BRCA1"))