R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ssviz)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: reshape
Attaching package: 'reshape'
The following objects are masked from 'package:S4Vectors':
expand, rename
Loading required package: ggplot2
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ssviz/plotPP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPP
> ### Title: plotPP
> ### Aliases: plotPP
>
> ### ** Examples
>
> data(ssviz)
> pp<-pingpong(pctrlbam)
No counts column provided in bam file. Running unique counts.
Otherwise provide a count matrix or run getCountMatrix.
Checking rnames:
L1_MM
L1_MM
***************
Unique forward reads: 299 , reverse reads: 201
Forward read # 1 out of 299
Forward read # 21 out of 299
Forward read # 41 out of 299
Forward read # 61 out of 299
Forward read # 81 out of 299
Forward read # 101 out of 299
Forward read # 121 out of 299
Forward read # 141 out of 299
Forward read # 161 out of 299
Forward read # 181 out of 299
Forward read # 201 out of 299
Forward read # 221 out of 299
Forward read # 241 out of 299
Forward read # 261 out of 299
Forward read # 281 out of 299
Done.
> plotPP(list(pp))
>
>
>
>
>
> dev.off()
null device
1
>