R: Methods for Function 'biasBoxplot' in Package 'EDASeq'
biasBoxplot-methods
R Documentation
Methods for Function biasBoxplot in Package EDASeq
Description
biasBoxplot produces a boxplot representing the distribution of a quantity of interest (e.g. gene counts, log-fold-changes, ...) stratified by a covariate (e.g. gene length, GC-contet, ...).
Usage
biasBoxplot(x,y,num.bins,...)
Arguments
x
A numeric vector with the quantity of interest (e.g. gene counts, log-fold-changes, ...)
y
A numeric vector with the covariate of interest (e.g. gene length, GC-contet, ...)
num.bins
A numeric value specifying the number of bins in wich to stratify y. Default to 10.
...
See par
Methods
signature(x = "numeric", y = "numeric", num.bins = "numeric")
It plots a line representing the regression of every column of the matrix x on the numeric covariate y. One can pass the usual graphical parameters as additional arguments (see par).
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(EDASeq)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ShortRead
Loading required package: BiocParallel
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
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/EDASeq/biasBoxplot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: biasBoxplot-methods
> ### Title: Methods for Function 'biasBoxplot' in Package 'EDASeq'
> ### Aliases: biasBoxplot biasBoxplot-methods
> ### biasBoxplot,numeric,numeric,numeric-method
> ### biasBoxplot,numeric,numeric-method
> ### Keywords: methods
>
> ### ** Examples
>
> library(yeastRNASeq)
> data(geneLevelData)
> data(yeastGC)
>
> sub <- intersect(rownames(geneLevelData), names(yeastGC))
>
> mat <- as.matrix(geneLevelData[sub,])
>
> data <- newSeqExpressionSet(mat,
+ phenoData=AnnotatedDataFrame(
+ data.frame(conditions=factor(c("mut", "mut", "wt", "wt")),
+ row.names=colnames(geneLevelData))),
+ featureData=AnnotatedDataFrame(data.frame(gc=yeastGC[sub])))
>
> lfc <- log(geneLevelData[sub, 3] + 1) - log(geneLevelData[sub, 1] + 1)
>
> biasBoxplot(lfc, yeastGC[sub], las=2, cex.axis=.7)
>
>
>
>
>
>
> dev.off()
null device
1
>