R: Methods for Function 'biasPlot' in Package 'EDASeq'
biasPlot-methods
R Documentation
Methods for Function biasPlot in Package EDASeq
Description
biasPlot produces a plot of the lowess regression of the counts on a covariate of interest, tipically the GC-content or the length of the genes.
Methods
signature(x = "matrix", y = "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).
signature(x = "SeqExpressionSet", y = "character")
It plots a line representing the regression of every lane in x on the covariate specified by y. y must be one of the column of the featureData slot of the x object. One can pass the usual graphical parameters as additional arguments (see par). The parameter color_code (optional) must be a number specifying the column of phenoData to be used for color-coding. By default it is color-coded according to the first column of phenoData. If legend=TRUE and col is not specified a legend with the information stored in phenoData is added.
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])))
biasPlot(data,"gc",ylim=c(0,5),log=TRUE)
Results
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/biasPlot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: biasPlot-methods
> ### Title: Methods for Function 'biasPlot' in Package 'EDASeq'
> ### Aliases: biasPlot biasPlot-methods biasPlot,matrix,numeric-method
> ### biasPlot,SeqExpressionSet,character-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])))
>
> biasPlot(data,"gc",ylim=c(0,5),log=TRUE)
>
>
>
>
>
>
> dev.off()
null device
1
>