Build a genome wide cut site map for a Restriction Enzyme (RE)

Description

Build a genome-wide cut map for a Restriction Enzyme (RE)

Usage

buildREmap(REpatternFilePath, format = "fasta", BSgenomeName, outfile)

Arguments

Value

Output REmap as a RangedData

Author(s)

Lihua Julie Zhu

Examples

	library(REDseq)
	REpatternFilePath = system.file("extdata", "examplePattern.fa", package="REDseq")
	library(BSgenome.Celegans.UCSC.ce2)
	buildREmap( REpatternFilePath, BSgenomeName=Celegans, outfile=tempfile())

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(REDseq)
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: BSgenome.Celegans.UCSC.ce2
Loading required package: BSgenome
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: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: multtest
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")'.

Loading required package: ChIPpeakAnno
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger

No methods found in "IRanges" for requests: %in%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/REDseq/buildREmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: buildREmap
> ### Title: Build a genome wide cut site map for a Restriction Enzyme (RE)
> ### Aliases: buildREmap
> ### Keywords: misc
> 
> ### ** Examples
> 
> 	library(REDseq)
> 	REpatternFilePath = system.file("extdata", "examplePattern.fa", package="REDseq")
> 	library(BSgenome.Celegans.UCSC.ce2)
> 	buildREmap( REpatternFilePath, BSgenomeName=Celegans, outfile=tempfile())
>>> Finding all hits in sequences chrI ...
>>> DONE searching
>>> Finding all hits in sequences chrII ...
>>> DONE searching
>>> Finding all hits in sequences chrIII ...
>>> DONE searching
>>> Finding all hits in sequences chrIV ...
>>> DONE searching
>>> Finding all hits in sequences chrV ...
>>> DONE searching
>>> Finding all hits in sequences chrX ...
>>> DONE searching
>>> Finding all hits in sequences chrM ...
>>> DONE searching
RangedData with 87959 rows and 2 value columns across 7 spaces
                          space               ranges   |      strand     score
                       <factor>            <IRanges>   | <character> <numeric>
ExampleRE.+.chrI.1            I       [ 1899,  1903]   |           +         1
ExampleRE.+.chrI.2            I       [ 6356,  6360]   |           +         1
ExampleRE.+.chrI.3            I       [ 6775,  6779]   |           +         1
ExampleRE.+.chrI.4            I       [ 6866,  6870]   |           +         1
ExampleRE.+.chrI.5            I       [11431, 11435]   |           +         1
ExampleRE.+.chrI.6            I       [11975, 11979]   |           +         1
ExampleRE.+.chrI.7            I       [12241, 12245]   |           +         1
ExampleRE.+.chrI.8            I       [13311, 13315]   |           +         1
ExampleRE.+.chrI.9            I       [14083, 14087]   |           +         1
...                         ...                  ... ...         ...       ...
ExampleRE.+.chrX.15068        X [17706097, 17706101]   |           +         1
ExampleRE.+.chrX.15069        X [17709329, 17709333]   |           +         1
ExampleRE.+.chrX.15070        X [17710564, 17710568]   |           +         1
ExampleRE.+.chrX.15071        X [17711033, 17711037]   |           +         1
ExampleRE.+.chrX.15072        X [17712037, 17712041]   |           +         1
ExampleRE.+.chrX.15073        X [17712181, 17712185]   |           +         1
ExampleRE.+.chrX.15074        X [17714984, 17714988]   |           +         1
ExampleRE.+.chrX.15075        X [17716980, 17716984]   |           +         1
ExampleRE.+.chrX.15076        X [17717264, 17717268]   |           +         1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>