The name of the input fasta format file, including
full path to file if it is located outside the current working directory
shapeList
A list containing four DNAshape prediction results
Value
Called for its effects
Note
None.
Author(s)
Tsu-Pei Chiu
Examples
fn2 <- system.file("extdata", "SingleSeqsample.fa", package = "DNAshapeR")
pred2 <- getShape(fn2)
trackShape(fn2, pred2) # Only for single sequence file
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 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(DNAshapeR)
Loading required package: GenomicRanges
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DNAshapeR/trackShape.Rd_%03d_medium.png", width=480, height=480)
> ### Name: trackShape
> ### Title: Plot track view of DNA shape features
> ### Aliases: trackShape
> ### Keywords: core
>
> ### ** Examples
>
> fn2 <- system.file("extdata", "SingleSeqsample.fa", package = "DNAshapeR")
> pred2 <- getShape(fn2)
Reading the input sequence......
Reading the input sequence......
Reading the input sequence......
Reading the input sequence......
Parsing files......
Read 2 items
Record length: 24
Read 2 items
Record length: 23
Read 2 items
Record length: 24
Read 2 items
Record length: 23
Done
> trackShape(fn2, pred2) # Only for single sequence file
Read 2 items
Read 1 item
>
>
>
>
>
> dev.off()
null device
1
>