R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(motifStack)
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
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
Attaching package: 'MotIV'
The following object is masked from 'package:stats':
filter
Loading required package: ade4
Attaching package: 'ade4'
The following object is masked from 'package:BiocGenerics':
score
Loading required package: Biostrings
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: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/motifStack/plotMotifLogoStack.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifLogoStack
> ### Title: plot sequence logos stack
> ### Aliases: plotMotifLogoStack
>
> ### ** Examples
>
> pcm1<-matrix(c(0,50,0,50,
+ 100,0,0,0,
+ 0,100,0,0,
+ 0,0,100,0,
+ 0,0,0,100,
+ 50,50,0,0,
+ 0,0,50,50), nrow=4)
> pcm2<-matrix(c(50,50,0,0,
+ 0,100,0,0,
+ 0,50,50,0,
+ 0,0,0,100,
+ 50,50,0,0,
+ 0,0,50,50), nrow=4)
> rownames(pcm1)<-c("A","C","G","T")
> rownames(pcm2)<-c("A","C","G","T")
> pfms<-list(p1=new("pfm",mat=pcm2pfm(pcm1),name="m1"),
+ p2=new("pfm",mat=pcm2pfm(pcm2),name="m2"))
> pfms<-DNAmotifAlignment(pfms)
> plotMotifLogoStack(pfms)
>
>
>
>
>
> dev.off()
null device
1
>