crunch-method: Fetching GRanges from various data source

In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

Description

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

Usage

## 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

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")

lawremi/biovizBase documentation built on Dec. 21, 2021, 9:42 a.m.