Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
function to visualize GC content or CpG content of input sequencesDescriptionplot.gc calculates the GC (or CpG) content based on a window size for each sequence and plots the content for all sequences as a heatmap over position and sequence. Usage## S4 method for signature 'cobindr' plot.gc(x, seq.ids, cpg = F, wind.size = 50, sig.test = F, hm.margin = c(4, 10), frac = 10, n.cpu = NA) Arguments
Author(s)Robert Lehmann <r.lehmann@biologie.hu-berlin.de> See Also
Examples
library(Biostrings)
n <- 50 # number of input sequences
l <- 100 # length of sequences
bases <- c("A","C","G","T") # alphabet
# generate random input sequences with two groups with differing GC content
seqs <- sapply(1:(3*n/4), function(x) paste(sample(bases, l, replace=TRUE,
prob=c(.3,.22,.2,.28)), collapse=""))
seqs <- append(seqs, sapply(1:(n/4), function(x) paste(sample(bases, l,
replace=TRUE, prob=c(.25,.25,.25,.25)), collapse="")))
#save sample sequences in fasta file
tmp.file <- tempfile(pattern = "cobindr_sample_seq", tmpdir = tempdir(),
fileext = ".fasta")
writeXStringSet(DNAStringSet(seqs), tmp.file)
cfg <- new('configuration')
slot(cfg, 'sequence_type') <- 'fasta'
slot(cfg, 'sequence_source') <- tmp.file
# avoid complaint of validation mechanism
slot(cfg, 'pfm_path') <- system.file('extdata/pfms',package='cobindR')
slot(cfg, 'pairs') <- ''
runObj <- new('cobindr', cfg, 'test')
plot.gc(runObj, cpg = TRUE)
unlink(tmp.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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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(cobindR)
Attaching package: 'cobindR'
The following object is masked from 'package:base':
sequence
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cobindR/plot.gc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.gc
> ### Title: function to visualize GC content or CpG content of input
> ### sequences
> ### Aliases: plot.gc plot.gc-method plot.gc,cobindr-method
> ### Keywords: dplot hplot
>
> ### ** Examples
>
> library(Biostrings)
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: XVector
>
> n <- 50 # number of input sequences
> l <- 100 # length of sequences
> bases <- c("A","C","G","T") # alphabet
> # generate random input sequences with two groups with differing GC content
> seqs <- sapply(1:(3*n/4), function(x) paste(sample(bases, l, replace=TRUE,
+ prob=c(.3,.22,.2,.28)), collapse=""))
> seqs <- append(seqs, sapply(1:(n/4), function(x) paste(sample(bases, l,
+ replace=TRUE, prob=c(.25,.25,.25,.25)), collapse="")))
> #save sample sequences in fasta file
> tmp.file <- tempfile(pattern = "cobindr_sample_seq", tmpdir = tempdir(),
+ fileext = ".fasta")
> writeXStringSet(DNAStringSet(seqs), tmp.file)
>
> cfg <- new('configuration')
Warning message:
In .local(.Object, ...) :
no config-file defined, generating configuration-object with default values
> slot(cfg, 'sequence_type') <- 'fasta'
> slot(cfg, 'sequence_source') <- tmp.file
> # avoid complaint of validation mechanism
> slot(cfg, 'pfm_path') <- system.file('extdata/pfms',package='cobindR')
> slot(cfg, 'pairs') <- ''
>
> runObj <- new('cobindr', cfg, 'test')
[1] "Creating a new experiment!"
reading file /tmp/Rtmp6Q7qNg/cobindr_sample_seq675a619ab566.fasta ...
| | | 0% | |= | 2% | |=== | 4% | |==== | 6% | |====== | 8% | |======= | 10% | |========= | 12% | |========== | 14% | |=========== | 16% | |============= | 18% | |============== | 20% | |================ | 22% | |================= | 24% | |=================== | 27% | |==================== | 29% | |===================== | 31% | |======================= | 33% | |======================== | 35% | |========================== | 37% | |=========================== | 39% | |============================= | 41% | |============================== | 43% | |=============================== | 45% | |================================= | 47% | |================================== | 49% | |==================================== | 51% | |===================================== | 53% | |======================================= | 55% | |======================================== | 57% | |========================================= | 59% | |=========================================== | 61% | |============================================ | 63% | |============================================== | 65% | |=============================================== | 67% | |================================================= | 69% | |================================================== | 71% | |=================================================== | 73% | |===================================================== | 76% | |====================================================== | 78% | |======================================================== | 80% | |========================================================= | 82% | |=========================================================== | 84% | |============================================================ | 86% | |============================================================= | 88% | |=============================================================== | 90% | |================================================================ | 92% | |================================================================== | 94% | |=================================================================== | 96% | |===================================================================== | 98% | |======================================================================| 100%ready retrieving sequences!
reading pfm files: /home/ddbj/local/lib64/R/library/cobindR/extdata/pfms ...
[1] "ES_Sox2_1_c1058"
[1] "ES_Klf4_3_c1373"
[1] "ES_Oct4_1_c570"
[1] "ES_Sox2_1_c1058"
ignored files:
Using the parallel (multicore) version of cobindR - function cpg.gc.content with 4 cores
There were 50 or more warnings (use warnings() to see the first 50)
>
> plot.gc(runObj, cpg = TRUE)
Loading required package: RColorBrewer
| | | 0%calculating GC / CpG content...
Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
[1] 1.5625
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[1] 0.9259259
| |=== | 4%Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
[1] 1.282051
| |==== | 6%Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
[1] 2.097902
| |====== | 8%Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
[1] 0.8333333
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[1] 0.7211538
| |========= | 12%Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
[1] 0.7142857
| |========== | 14%Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
[1] 0.4545455
| |=========== | 16%Using the parallel (multicore) version of cobindR - function wind.cpg.content with 4 cores
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[1] 0.4201681
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[1] 0.9615385
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[1] 1.25
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[1] 1.470588
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[1] 1.25
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>
> unlink(tmp.file)
>
>
>
>
>
> dev.off()
null device
1
>
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and