Separate a TranscriptDb object based on a chromosome.

Description

With the isActiveSeq method in GenomicFeatures package, this function filters the transcriptDb object in the GenomicFeatures package based on a single chromosome.

Usage

chrseparate(transdb = NULL, chrname = NULL)

Arguments

Value

This function returns the TrnascriptDb limited to the chromosome number that you want.

Author(s)

Seonggyun Han, Sangsoo Kim

References

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Morgan M, and Carey V. Software for Computing and Annotating Genomic Ranges. PLoS Computational Biology, 9, e1003118. 2013.

See Also

isActiveSeq, seqinfo

Examples

sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
sample.Txdb <- loadDb(sampleDB)
filtered.txdb <- chrseparate(sample.Txdb,19)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(IVAS)
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")'.

No methods found in "BiocGenerics" for requests: unlist
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IVAS/chrseparate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chrseparate
> ### Title: Separate a TranscriptDb object based on a chromosome.
> ### Aliases: chrseparate
> 
> ### ** Examples
> 
> sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
> sample.Txdb <- loadDb(sampleDB)
> filtered.txdb <- chrseparate(sample.Txdb,19)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>