Fetching GRanges from various data source

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

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(biovizBase)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biovizBase/crunch-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: crunch
> ### Title: Fetching GRanges from various data source
> ### Aliases: crunch crunch,TxDb-method crunch,EnsDb-method
> ###   crunch,GAlignments-method crunch,BamFile-method
> 
> ### ** Examples
> 
> library(biovizBase)
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
Loading required package: 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")'.

> data(genesymbol, package = "biovizBase")
> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> obj <- txdb
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "all")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
> temp <- crunch(txdb, which = genesymbol["BRCA1"], type = "reduce")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
> 
> ## Fetching data from a EnsDb object.
> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
> edb <- EnsDb.Hsapiens.v75
> gr <- genesymbol["BRCA1"]
> seqlevels(gr) <- sub(seqlevels(gr), pattern="chr", replacement="")
> temp <- crunch(edb, which=gr)
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
Warning messages:
1: In if (!is.na(genome(which))) { :
  the condition has length > 1 and only the first element will be used
2: In if (!(seqlevels(which) %in% seqlevels(obj))) stop(seqlevels(which),  :
  the condition has length > 1 and only the first element will be used
> 
> ## Alternatively, use the GenenameFilter from the ensembldb package:
> temp <- crunch(edb, which=GenenameFilter("BRCA1"))
Fetching data...OK
Parsing exons...OK
Defining introns...OK
Defining UTRs...OK
Defining CDS...OK
aggregating...
Done
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>