crunch-method: Fetching GRanges from various data source

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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## S4 method for signature 'TxDb'
crunch(obj, which, columns = c("tx_id", "tx_name","gene_id"),
       type = c("all", "reduce"), truncate.gaps = FALSE,
       truncate.fun = NULL, ratio = 0.0025)
## S4 method for signature 'EnsDb'
crunch(obj, which, columns = c("tx_id", "gene_name","gene_id"),
       type = c("all", "reduce"), truncate.gaps = FALSE,
       truncate.fun = NULL, ratio = 0.0025)
## S4 method for signature 'GAlignments'
crunch(obj, which, truncate.gaps = FALSE,
       truncate.fun = NULL, ratio = 0.0025)
## S4 method for signature 'BamFile'
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 AnnotationFilter-class, an AnnotationFilterList combining several such objects or a filter expression in form of a formula (see AnnotationFilter for examples).

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.

Author(s)

Tengfei Yin

Examples

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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 AnnotationFilter package:
temp <- crunch(edb, which = GenenameFilter("BRCA1"))

## Or a filter expression
temp <- crunch(edb, which = ~ genename == "BRCA1")

Bioconductor-mirror/biovizBase documentation built on June 1, 2017, 5:21 a.m.