Last data update: 2014.03.03
R: Intermediate data of the analysis pipeline
datamatrixTransformed R Documentation
Intermediate data of the analysis pipeline
Description
Glog transformed feature data represented as a list
containing
array
D
and list
anno
.
Usage
data(datamatrixTransformed)
Format
List of 2
$ D : num [1:1372, 1:12, 1:2, 1:385]
$ anno:List of 4
..$ drug:'data.frame': 1372 obs. of 15 variables
..$ line:'data.frame': 12 obs. of 4 variables
..$ repl: int [1:2]
..$ ftr : chr [1:385]
Value
The four dimensional array
D
contains the glog transformed feature
data which were rearanged from the original ftrs
data.frame
.
The dimensions represent:
drug
cell line
replicate
feature
The annotation anno
is represented as a list
containing a
data.frame
drug
with the drug annotation, a data.frame
line
with the cell line annotation, a vector
repl
with the
information about the replicates and a vector
ftr
with the
feature names.
Examples
data(datamatrixTransformed)
str(datamatrixTransformed)
Results
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(PGPC)
Loading required package: EBImage
Loading required package: imageHTS
Loading required package: cellHTS2
Loading required package: RColorBrewer
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")'.
Attaching package: 'Biobase'
The following object is masked from 'package:EBImage':
channel
Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: grid
Loading required package: SearchTrees
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following object is masked from 'package:cellHTS2':
annotate
Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:gplots':
space
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Attaching package: 'IRanges'
The following objects are masked from 'package:EBImage':
resize, tile
Loading required package: XML
Loading required package: ChemmineR
Attaching package: 'ChemmineR'
The following object is masked from 'package:S4Vectors':
fold
The following object is masked from 'package:limma':
makeUnique
Loading required package: reshape2
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGPC/datamatrixTransformed.Rd_%03d_medium.png", width=480, height=480)
> ### Name: datamatrixTransformed
> ### Title: Intermediate data of the analysis pipeline
> ### Aliases: datamatrixTransformed
> ### Keywords: datasets
>
> ### ** Examples
>
> data(datamatrixTransformed)
> str(datamatrixTransformed)
List of 2
$ D : num [1:1372, 1:12, 1:2, 1:385] 11.9 12 11.9 12 12 ...
$ anno:List of 4
..$ drug:'data.frame': 1372 obs. of 15 variables:
.. ..$ PlateName : chr [1:1372] "P1" "P1" "P1" "P1" ...
.. ..$ Well : chr [1:1372] "A03" "A04" "A05" "A06" ...
.. ..$ Content : chr [1:1372] "sample" "sample" "sample" "sample" ...
.. ..$ compoundID_384 : chr [1:1372] "78875" "78955" "78876" "78956" ...
.. ..$ compoundID : chr [1:1372] "78875" "78955" "78876" "78956" ...
.. ..$ mol.weight.Structure: chr [1:1372] "195,22001" "163,19638" "202,25818" "131,17601" ...
.. ..$ Name : chr [1:1372] "DL-alpha-Methyl-p-tyrosine" "N-Acetyl-L-Cysteine" "6-Methoxy-1,2,3,4-tetrahydro-9H-pyrido[3,4b] indole" "6-Aminohexanoic acid" ...
.. ..$ SecName : chr [1:1372] "4-Hydroxy-alpha-methylphenylalanine" "" "" "6-Aminocaproic acid; EACA" ...
.. ..$ Class : chr [1:1372] "Neurotransmission" "Glutamate" "Neurotransmission" "Immune System" ...
.. ..$ Enzyme : chr [1:1372] "Enzyme" "" "Enzyme" "" ...
.. ..$ Action : chr [1:1372] "Inhibitor" "Antagonist" "Inhibitor" "Inhibitor" ...
.. ..$ Selectivity : chr [1:1372] "Tyrosine hydroxylase" "" "MAO" "Blood Clotting" ...
.. ..$ Description : chr [1:1372] "Inhibitor of catecholamine synthesis and tyrosine hydroxylase" "Amino acid analog that partially improves neuronal survival following transient forebrain ischemia" "MAO inhibitor" "Promotes rapid dissociation of plasmin, thereby inhibiting the activation of plasminogen and subsequent fibrinolysis; inhibits "| __truncated__ ...
.. ..$ GeneID : chr [1:1372] "78875" "78955" "78876" "78956" ...
.. ..$ Selectivity_updated : chr [1:1372] "Tyrosine hydroxylase" "AA-analog" "MAO" "Blood Clotting" ...
..$ line:'data.frame': 12 obs. of 4 variables:
.. ..$ name : chr [1:12] "02-006" "02-031" "02-004" "104-009" ...
.. ..$ mutationDetailed: chr [1:12] "AKT1-/-&AKT2-/-" "MEK2-/-" "AKT1-/-" "CTNNB1 mt-/wt+" ...
.. ..$ mutation : chr [1:12] "AKT1/2" "MEK2" "AKT1" "CTNNB1 wt" ...
.. ..$ startPlate : num [1:12] 1 5 9 13 17 21 25 29 33 37 ...
..$ repl: int [1:2] 1 2
..$ ftr : chr [1:385] "n" "nseg.0.m.cx.mean" "nseg.0.m.cy.mean" "nseg.0.m.majoraxis.mean" ...
>
>
>
>
>
> dev.off()
null device
1
>