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.
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 table listing the number of features showing a monotone
titration response and a figure showing the proportion
of features showing a monotone titration response vs the difference in
pure sample expression.
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.
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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/titrationResponse.Rd_%03d_medium.png", width=480, height=480)
> ### Name: titrationResponse
> ### Title: Assess monotone signal across titration
> ### Aliases: titrationResponse
> ### Keywords: manip
>
> ### ** Examples
>
> data(lifetech)
> titrationResponse(object1=lifetech,qcThreshold1=1.25)
A B
Mono 98 164
Non-Mono 109 43
> data(qpcRdefault)
> titrationResponse(object1=lifetech,qcThreshold1=1.25,
+ object2=qpcRdefault,qcThreshold2=0.99)
Method 1:A Method 2:A Method 1:B Method 2:B
Mono 96 84 163 161
Non-Mono 108 120 41 43
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
