a list containing two elements: ct (the expression
estiamtes) and qc (quality scores)
qcThreshold1
a numeric threshold corresponding to object1$qc
below which values are considered low quality.
object2
an optional second list of the same format as
object1, used to compare two methods.
qcThreshold2
a numeric threshold corresponding to object2$qc
below which values are considered low quality.
commonFeatures
if TRUE and object2 is non-NULL, only high quality non-NA features in common between both objects are used.
statistic
whether to compute the standard deviation (sd) or
coefficient of variation (cv).
scale
optional scaling of the values. This can help with
visualizing the distributions.
bins
the number of bins to divide the data into.
label1
optional label corresponding to object 1 to be used in plotting.
label2
optional label corresponding to object 2 to be used in plotting.
Value
A boxplot of either the standard deviation or coefficient of variation
stratified by expression is produced. The values plotted in each box
of the boxplot are returned.
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
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Type 'q()' to quit R.
> library(miRcomp)
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: miRcompData
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/miRcomp/precision.Rd_%03d_medium.png", width=480, height=480)
> ### Name: precision
> ### Title: Assess the precision of the expression estimates
> ### Aliases: precision
> ### Keywords: manip
>
> ### ** Examples
>
> data(lifetech)
> tmp1 <- precision(object1=lifetech,qcThreshold1=1.25)
> data(qpcRdefault)
> tmp2 <- precision(object1=lifetech,qcThreshold1=1.25,
+ object2=qpcRdefault,qcThreshold2=0.99)
>
>
>
>
>
> dev.off()
null device
1
>