Output count/weight summary by restriction enzyme cut site ID (REid)

Description

Output count/weight summary by REid with each row representing each REid

Usage

summarizeByRE(assignedSeqs, by=c("Weight", "REid"),sampleName="",round=TRUE)

Arguments

Value

a matrix with REid as the first column and total count/weight as the second column, that can be used for the downstream analysis with DEseq or edgeR.

Author(s)

Lihua Julie Zhu

See Also

summarizeBySeq, assignSeq2REsite

Examples

	library(REDseq)
	data(example.assignedREDseq)
	summarizeByRE(example.assignedREDseq,by="REid",sampleName="example")
	summarizeByRE(example.assignedREDseq,by="Weight",sampleName="example")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/summarizeByRE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summarizeByRE
> ### Title: Output count/weight summary by restriction enzyme cut site ID
> ###   (REid)
> ### Aliases: summarizeByRE
> ### Keywords: misc
> 
> ### ** Examples
> 
> 	library(REDseq)
> 	data(example.assignedREDseq)
> 	summarizeByRE(example.assignedREDseq,by="REid",sampleName="example")
              REid example
1  Sau96I.chr10.29       4
2  Sau96I.chr10.30       3
3  Sau96I.chr10.40       2
4  Sau96I.chr10.42       9
5  Sau96I.chr10.43       7
6  Sau96I.chr10.45       4
7  Sau96I.chr10.47       3
8  Sau96I.chr10.49       3
9  Sau96I.chr10.50       5
10 Sau96I.chr10.51       4
> 	summarizeByRE(example.assignedREDseq,by="Weight",sampleName="example")
                REid              example
Sau96I.chr10.29 "Sau96I.chr10.29" "4"    
Sau96I.chr10.30 "Sau96I.chr10.30" "2"    
Sau96I.chr10.40 "Sau96I.chr10.40" "1"    
Sau96I.chr10.42 "Sau96I.chr10.42" "9"    
Sau96I.chr10.43 "Sau96I.chr10.43" "6"    
Sau96I.chr10.45 "Sau96I.chr10.45" "3"    
Sau96I.chr10.47 "Sau96I.chr10.47" "1"    
Sau96I.chr10.49 "Sau96I.chr10.49" "1"    
Sau96I.chr10.50 "Sau96I.chr10.50" "3"    
Sau96I.chr10.51 "Sau96I.chr10.51" "2"    
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>