a list containing two elements: ct (the expression
estimates) 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.
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 plot of signal detect slopes stratified by difference in pure sample
expression is produced, and a summary (median and MAD) of the signal
detect slopes in each bin is 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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> 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/accuracy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: accuracy
> ### Title: Assess the accuracy of the expression estimates
> ### Aliases: accuracy
> ### Keywords: manip
>
> ### ** Examples
>
> data(lifetech)
> accuracy(object1=lifetech,qcThreshold1=1.25)
bin1 bin2 bin3
Bin "(-0.0983,0.942]" "(0.942,1.97]" "(1.97,11.7]"
Median "0.85" "0.9" "0.9"
MAD "0.28" "0.18" "0.14"
> data(qpcRdefault)
> accuracy(object1=lifetech,qcThreshold1=1.25,
+ object2=qpcRdefault,qcThreshold2=0.99)
$M1
bin1 bin2 bin3
Bin "(-0.0983,0.916]" "(0.916,1.95]" "(1.95,11.7]"
Median "0.85" "0.91" "0.9"
MAD "0.32" "0.19" "0.14"
$M2
bin1 bin2 bin3
Bin "(-0.095,0.964]" "(0.964,2.07]" "(2.07,12]"
Median "0.86" "0.95" "0.95"
MAD "0.34" "0.2" "0.15"
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
