Last data update: 2014.03.03
R: Well profiles extracted from images using imageHTS
Well profiles extracted from images using imageHTS
Description
This file contains the data.frame
output of the imageHTS
pipeline.
Usage
data(ftrs)
Format
A data frame with 36864 observations on 396 variables.
The first is 'uname
', a character vector of the well unames.
The remaining 395 variables are numeric vectors of feature summaries
for each well.
Value
Feature summaries calculated over all features extracted from the cells in each
well. The wells are defined by their uname
.
See Also
extractFeatures
, computeFeatures
,
getFeaturesAllSpots
, summarizeWellsExtended
Examples
data(ftrs)
names(ftrs)
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/ftrs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ftrs
> ### Title: Well profiles extracted from images using imageHTS
> ### Aliases: ftrs
> ### Keywords: datasets
>
> ### ** Examples
>
> data(ftrs)
> names(ftrs)
[1] "uname" "n"
[3] "nseg.0.m.cx.mean" "nseg.0.m.cy.mean"
[5] "nseg.0.m.majoraxis.mean" "nseg.0.m.eccentricity.mean"
[7] "nseg.0.m.theta.mean" "nseg.0.s.area.mean"
[9] "nseg.0.s.perimeter.mean" "nseg.0.s.radius.mean.mean"
[11] "nseg.0.s.radius.min.mean" "nseg.0.s.radius.max.mean"
[13] "nseg.dna.b.mean.mean" "nseg.dna.b.sd.mean"
[15] "nseg.dna.b.mad.mean" "nseg.dna.m.cx.mean"
[17] "nseg.dna.m.cy.mean" "nseg.dna.m.majoraxis.mean"
[19] "nseg.dna.m.eccentricity.mean" "nseg.dna.m.theta.mean"
[21] "nseg.dna.h.asm.s1.mean" "nseg.dna.h.con.s1.mean"
[23] "nseg.dna.h.cor.s1.mean" "nseg.dna.h.var.s1.mean"
[25] "nseg.dna.h.idm.s1.mean" "nseg.dna.h.sav.s1.mean"
[27] "nseg.dna.h.sva.s1.mean" "nseg.dna.h.sen.s1.mean"
[29] "nseg.dna.h.ent.s1.mean" "nseg.dna.h.dva.s1.mean"
[31] "nseg.dna.h.den.s1.mean" "nseg.dna.h.f12.s1.mean"
[33] "nseg.dna.h.f13.s1.mean" "nseg.dna.h.asm.s2.mean"
[35] "nseg.dna.h.con.s2.mean" "nseg.dna.h.cor.s2.mean"
[37] "nseg.dna.h.var.s2.mean" "nseg.dna.h.idm.s2.mean"
[39] "nseg.dna.h.sav.s2.mean" "nseg.dna.h.sva.s2.mean"
[41] "nseg.dna.h.sen.s2.mean" "nseg.dna.h.ent.s2.mean"
[43] "nseg.dna.h.dva.s2.mean" "nseg.dna.h.den.s2.mean"
[45] "nseg.dna.h.f12.s2.mean" "nseg.dna.h.f13.s2.mean"
[47] "cseg.0.m.cx.mean" "cseg.0.m.cy.mean"
[49] "cseg.0.m.majoraxis.mean" "cseg.0.m.eccentricity.mean"
[51] "cseg.0.m.theta.mean" "cseg.0.s.area.mean"
[53] "cseg.0.s.perimeter.mean" "cseg.0.s.radius.mean.mean"
[55] "cseg.0.s.radius.min.mean" "cseg.0.s.radius.max.mean"
[57] "cseg.act.b.mean.mean" "cseg.act.b.sd.mean"
[59] "cseg.act.b.mad.mean" "cseg.act.m.cx.mean"
[61] "cseg.act.m.cy.mean" "cseg.act.m.majoraxis.mean"
[63] "cseg.act.m.eccentricity.mean" "cseg.act.m.theta.mean"
[65] "cseg.act.h.asm.s1.mean" "cseg.act.h.con.s1.mean"
[67] "cseg.act.h.cor.s1.mean" "cseg.act.h.var.s1.mean"
[69] "cseg.act.h.idm.s1.mean" "cseg.act.h.sav.s1.mean"
[71] "cseg.act.h.sva.s1.mean" "cseg.act.h.sen.s1.mean"
[73] "cseg.act.h.ent.s1.mean" "cseg.act.h.dva.s1.mean"
[75] "cseg.act.h.den.s1.mean" "cseg.act.h.f12.s1.mean"
[77] "cseg.act.h.f13.s1.mean" "cseg.act.h.asm.s2.mean"
[79] "cseg.act.h.con.s2.mean" "cseg.act.h.cor.s2.mean"
[81] "cseg.act.h.var.s2.mean" "cseg.act.h.idm.s2.mean"
[83] "cseg.act.h.sav.s2.mean" "cseg.act.h.sva.s2.mean"
[85] "cseg.act.h.sen.s2.mean" "cseg.act.h.ent.s2.mean"
[87] "cseg.act.h.dva.s2.mean" "cseg.act.h.den.s2.mean"
[89] "cseg.act.h.f12.s2.mean" "cseg.act.h.f13.s2.mean"
[91] "cseg.dnaact.b.mean.mean" "cseg.dnaact.b.sd.mean"
[93] "cseg.dnaact.b.mad.mean" "cseg.dnaact.m.cx.mean"
[95] "cseg.dnaact.m.cy.mean" "cseg.dnaact.m.majoraxis.mean"
[97] "cseg.dnaact.m.eccentricity.mean" "cseg.dnaact.m.theta.mean"
[99] "cseg.dnaact.h.asm.s1.mean" "cseg.dnaact.h.con.s1.mean"
[101] "cseg.dnaact.h.cor.s1.mean" "cseg.dnaact.h.var.s1.mean"
[103] "cseg.dnaact.h.idm.s1.mean" "cseg.dnaact.h.sav.s1.mean"
[105] "cseg.dnaact.h.sva.s1.mean" "cseg.dnaact.h.sen.s1.mean"
[107] "cseg.dnaact.h.ent.s1.mean" "cseg.dnaact.h.dva.s1.mean"
[109] "cseg.dnaact.h.den.s1.mean" "cseg.dnaact.h.f12.s1.mean"
[111] "cseg.dnaact.h.f13.s1.mean" "cseg.dnaact.h.asm.s2.mean"
[113] "cseg.dnaact.h.con.s2.mean" "cseg.dnaact.h.cor.s2.mean"
[115] "cseg.dnaact.h.var.s2.mean" "cseg.dnaact.h.idm.s2.mean"
[117] "cseg.dnaact.h.sav.s2.mean" "cseg.dnaact.h.sva.s2.mean"
[119] "cseg.dnaact.h.sen.s2.mean" "cseg.dnaact.h.ent.s2.mean"
[121] "cseg.dnaact.h.dva.s2.mean" "cseg.dnaact.h.den.s2.mean"
[123] "cseg.dnaact.h.f12.s2.mean" "cseg.dnaact.h.f13.s2.mean"
[125] "lcd.10NN.mean" "lcd.15NN.mean"
[127] "lcd.20NN.mean" "nseg.0.m.cx.sd"
[129] "nseg.0.m.cy.sd" "nseg.0.m.majoraxis.sd"
[131] "nseg.0.m.eccentricity.sd" "nseg.0.m.theta.sd"
[133] "nseg.0.s.area.sd" "nseg.0.s.perimeter.sd"
[135] "nseg.0.s.radius.mean.sd" "nseg.0.s.radius.min.sd"
[137] "nseg.0.s.radius.max.sd" "nseg.dna.b.mean.sd"
[139] "nseg.dna.b.sd.sd" "nseg.dna.b.mad.sd"
[141] "nseg.dna.m.cx.sd" "nseg.dna.m.cy.sd"
[143] "nseg.dna.m.majoraxis.sd" "nseg.dna.m.eccentricity.sd"
[145] "nseg.dna.m.theta.sd" "nseg.dna.h.asm.s1.sd"
[147] "nseg.dna.h.con.s1.sd" "nseg.dna.h.cor.s1.sd"
[149] "nseg.dna.h.var.s1.sd" "nseg.dna.h.idm.s1.sd"
[151] "nseg.dna.h.sav.s1.sd" "nseg.dna.h.sva.s1.sd"
[153] "nseg.dna.h.sen.s1.sd" "nseg.dna.h.ent.s1.sd"
[155] "nseg.dna.h.dva.s1.sd" "nseg.dna.h.den.s1.sd"
[157] "nseg.dna.h.f12.s1.sd" "nseg.dna.h.f13.s1.sd"
[159] "nseg.dna.h.asm.s2.sd" "nseg.dna.h.con.s2.sd"
[161] "nseg.dna.h.cor.s2.sd" "nseg.dna.h.var.s2.sd"
[163] "nseg.dna.h.idm.s2.sd" "nseg.dna.h.sav.s2.sd"
[165] "nseg.dna.h.sva.s2.sd" "nseg.dna.h.sen.s2.sd"
[167] "nseg.dna.h.ent.s2.sd" "nseg.dna.h.dva.s2.sd"
[169] "nseg.dna.h.den.s2.sd" "nseg.dna.h.f12.s2.sd"
[171] "nseg.dna.h.f13.s2.sd" "cseg.0.m.cx.sd"
[173] "cseg.0.m.cy.sd" "cseg.0.m.majoraxis.sd"
[175] "cseg.0.m.eccentricity.sd" "cseg.0.m.theta.sd"
[177] "cseg.0.s.area.sd" "cseg.0.s.perimeter.sd"
[179] "cseg.0.s.radius.mean.sd" "cseg.0.s.radius.min.sd"
[181] "cseg.0.s.radius.max.sd" "cseg.act.b.mean.sd"
[183] "cseg.act.b.sd.sd" "cseg.act.b.mad.sd"
[185] "cseg.act.m.cx.sd" "cseg.act.m.cy.sd"
[187] "cseg.act.m.majoraxis.sd" "cseg.act.m.eccentricity.sd"
[189] "cseg.act.m.theta.sd" "cseg.act.h.asm.s1.sd"
[191] "cseg.act.h.con.s1.sd" "cseg.act.h.cor.s1.sd"
[193] "cseg.act.h.var.s1.sd" "cseg.act.h.idm.s1.sd"
[195] "cseg.act.h.sav.s1.sd" "cseg.act.h.sva.s1.sd"
[197] "cseg.act.h.sen.s1.sd" "cseg.act.h.ent.s1.sd"
[199] "cseg.act.h.dva.s1.sd" "cseg.act.h.den.s1.sd"
[201] "cseg.act.h.f12.s1.sd" "cseg.act.h.f13.s1.sd"
[203] "cseg.act.h.asm.s2.sd" "cseg.act.h.con.s2.sd"
[205] "cseg.act.h.cor.s2.sd" "cseg.act.h.var.s2.sd"
[207] "cseg.act.h.idm.s2.sd" "cseg.act.h.sav.s2.sd"
[209] "cseg.act.h.sva.s2.sd" "cseg.act.h.sen.s2.sd"
[211] "cseg.act.h.ent.s2.sd" "cseg.act.h.dva.s2.sd"
[213] "cseg.act.h.den.s2.sd" "cseg.act.h.f12.s2.sd"
[215] "cseg.act.h.f13.s2.sd" "cseg.dnaact.b.mean.sd"
[217] "cseg.dnaact.b.sd.sd" "cseg.dnaact.b.mad.sd"
[219] "cseg.dnaact.m.cx.sd" "cseg.dnaact.m.cy.sd"
[221] "cseg.dnaact.m.majoraxis.sd" "cseg.dnaact.m.eccentricity.sd"
[223] "cseg.dnaact.m.theta.sd" "cseg.dnaact.h.asm.s1.sd"
[225] "cseg.dnaact.h.con.s1.sd" "cseg.dnaact.h.cor.s1.sd"
[227] "cseg.dnaact.h.var.s1.sd" "cseg.dnaact.h.idm.s1.sd"
[229] "cseg.dnaact.h.sav.s1.sd" "cseg.dnaact.h.sva.s1.sd"
[231] "cseg.dnaact.h.sen.s1.sd" "cseg.dnaact.h.ent.s1.sd"
[233] "cseg.dnaact.h.dva.s1.sd" "cseg.dnaact.h.den.s1.sd"
[235] "cseg.dnaact.h.f12.s1.sd" "cseg.dnaact.h.f13.s1.sd"
[237] "cseg.dnaact.h.asm.s2.sd" "cseg.dnaact.h.con.s2.sd"
[239] "cseg.dnaact.h.cor.s2.sd" "cseg.dnaact.h.var.s2.sd"
[241] "cseg.dnaact.h.idm.s2.sd" "cseg.dnaact.h.sav.s2.sd"
[243] "cseg.dnaact.h.sva.s2.sd" "cseg.dnaact.h.sen.s2.sd"
[245] "cseg.dnaact.h.ent.s2.sd" "cseg.dnaact.h.dva.s2.sd"
[247] "cseg.dnaact.h.den.s2.sd" "cseg.dnaact.h.f12.s2.sd"
[249] "cseg.dnaact.h.f13.s2.sd" "lcd.10NN.sd"
[251] "lcd.15NN.sd" "lcd.20NN.sd"
[253] "nseg.0.m.cx.qt.0.01" "nseg.0.m.cx.qt.0.05"
[255] "nseg.0.m.cx.qt.0.95" "nseg.0.m.cx.qt.0.99"
[257] "nseg.0.m.cy.qt.0.01" "nseg.0.m.cy.qt.0.05"
[259] "nseg.0.m.cy.qt.0.95" "nseg.0.m.cy.qt.0.99"
[261] "nseg.0.m.majoraxis.qt.0.01" "nseg.0.m.majoraxis.qt.0.05"
[263] "nseg.0.m.majoraxis.qt.0.95" "nseg.0.m.majoraxis.qt.0.99"
[265] "nseg.0.m.eccentricity.qt.0.01" "nseg.0.m.eccentricity.qt.0.05"
[267] "nseg.0.m.eccentricity.qt.0.95" "nseg.0.m.eccentricity.qt.0.99"
[269] "nseg.0.s.area.qt.0.01" "nseg.0.s.area.qt.0.05"
[271] "nseg.0.s.area.qt.0.95" "nseg.0.s.area.qt.0.99"
[273] "nseg.0.s.perimeter.qt.0.01" "nseg.0.s.perimeter.qt.0.05"
[275] "nseg.0.s.perimeter.qt.0.95" "nseg.0.s.perimeter.qt.0.99"
[277] "nseg.0.s.radius.mean.qt.0.01" "nseg.0.s.radius.mean.qt.0.05"
[279] "nseg.0.s.radius.mean.qt.0.95" "nseg.0.s.radius.mean.qt.0.99"
[281] "nseg.0.s.radius.min.qt.0.01" "nseg.0.s.radius.min.qt.0.05"
[283] "nseg.0.s.radius.min.qt.0.95" "nseg.0.s.radius.min.qt.0.99"
[285] "nseg.0.s.radius.max.qt.0.01" "nseg.0.s.radius.max.qt.0.05"
[287] "nseg.0.s.radius.max.qt.0.95" "nseg.0.s.radius.max.qt.0.99"
[289] "nseg.dna.b.mean.qt.0.01" "nseg.dna.b.mean.qt.0.05"
[291] "nseg.dna.b.mean.qt.0.95" "nseg.dna.b.mean.qt.0.99"
[293] "nseg.dna.m.cx.qt.0.01" "nseg.dna.m.cx.qt.0.05"
[295] "nseg.dna.m.cx.qt.0.95" "nseg.dna.m.cx.qt.0.99"
[297] "nseg.dna.m.cy.qt.0.01" "nseg.dna.m.cy.qt.0.05"
[299] "nseg.dna.m.cy.qt.0.95" "nseg.dna.m.cy.qt.0.99"
[301] "nseg.dna.m.majoraxis.qt.0.01" "nseg.dna.m.majoraxis.qt.0.05"
[303] "nseg.dna.m.majoraxis.qt.0.95" "nseg.dna.m.majoraxis.qt.0.99"
[305] "nseg.dna.m.eccentricity.qt.0.01" "nseg.dna.m.eccentricity.qt.0.05"
[307] "nseg.dna.m.eccentricity.qt.0.95" "nseg.dna.m.eccentricity.qt.0.99"
[309] "cseg.0.m.cx.qt.0.01" "cseg.0.m.cx.qt.0.05"
[311] "cseg.0.m.cx.qt.0.95" "cseg.0.m.cx.qt.0.99"
[313] "cseg.0.m.cy.qt.0.01" "cseg.0.m.cy.qt.0.05"
[315] "cseg.0.m.cy.qt.0.95" "cseg.0.m.cy.qt.0.99"
[317] "cseg.0.m.majoraxis.qt.0.01" "cseg.0.m.majoraxis.qt.0.05"
[319] "cseg.0.m.majoraxis.qt.0.95" "cseg.0.m.majoraxis.qt.0.99"
[321] "cseg.0.m.eccentricity.qt.0.01" "cseg.0.m.eccentricity.qt.0.05"
[323] "cseg.0.m.eccentricity.qt.0.95" "cseg.0.m.eccentricity.qt.0.99"
[325] "cseg.0.s.area.qt.0.01" "cseg.0.s.area.qt.0.05"
[327] "cseg.0.s.area.qt.0.95" "cseg.0.s.area.qt.0.99"
[329] "cseg.0.s.perimeter.qt.0.01" "cseg.0.s.perimeter.qt.0.05"
[331] "cseg.0.s.perimeter.qt.0.95" "cseg.0.s.perimeter.qt.0.99"
[333] "cseg.0.s.radius.mean.qt.0.01" "cseg.0.s.radius.mean.qt.0.05"
[335] "cseg.0.s.radius.mean.qt.0.95" "cseg.0.s.radius.mean.qt.0.99"
[337] "cseg.0.s.radius.min.qt.0.01" "cseg.0.s.radius.min.qt.0.05"
[339] "cseg.0.s.radius.min.qt.0.95" "cseg.0.s.radius.min.qt.0.99"
[341] "cseg.0.s.radius.max.qt.0.01" "cseg.0.s.radius.max.qt.0.05"
[343] "cseg.0.s.radius.max.qt.0.95" "cseg.0.s.radius.max.qt.0.99"
[345] "cseg.act.b.mean.qt.0.01" "cseg.act.b.mean.qt.0.05"
[347] "cseg.act.b.mean.qt.0.95" "cseg.act.b.mean.qt.0.99"
[349] "cseg.act.m.cx.qt.0.01" "cseg.act.m.cx.qt.0.05"
[351] "cseg.act.m.cx.qt.0.95" "cseg.act.m.cx.qt.0.99"
[353] "cseg.act.m.cy.qt.0.01" "cseg.act.m.cy.qt.0.05"
[355] "cseg.act.m.cy.qt.0.95" "cseg.act.m.cy.qt.0.99"
[357] "cseg.act.m.majoraxis.qt.0.01" "cseg.act.m.majoraxis.qt.0.05"
[359] "cseg.act.m.majoraxis.qt.0.95" "cseg.act.m.majoraxis.qt.0.99"
[361] "cseg.act.m.eccentricity.qt.0.01" "cseg.act.m.eccentricity.qt.0.05"
[363] "cseg.act.m.eccentricity.qt.0.95" "cseg.act.m.eccentricity.qt.0.99"
[365] "cseg.dnaact.b.mean.qt.0.01" "cseg.dnaact.b.mean.qt.0.05"
[367] "cseg.dnaact.b.mean.qt.0.95" "cseg.dnaact.b.mean.qt.0.99"
[369] "cseg.dnaact.m.cx.qt.0.01" "cseg.dnaact.m.cx.qt.0.05"
[371] "cseg.dnaact.m.cx.qt.0.95" "cseg.dnaact.m.cx.qt.0.99"
[373] "cseg.dnaact.m.cy.qt.0.01" "cseg.dnaact.m.cy.qt.0.05"
[375] "cseg.dnaact.m.cy.qt.0.95" "cseg.dnaact.m.cy.qt.0.99"
[377] "cseg.dnaact.m.majoraxis.qt.0.01" "cseg.dnaact.m.majoraxis.qt.0.05"
[379] "cseg.dnaact.m.majoraxis.qt.0.95" "cseg.dnaact.m.majoraxis.qt.0.99"
[381] "cseg.dnaact.m.eccentricity.qt.0.01" "cseg.dnaact.m.eccentricity.qt.0.05"
[383] "cseg.dnaact.m.eccentricity.qt.0.95" "cseg.dnaact.m.eccentricity.qt.0.99"
[385] "lcd.10NN.qt.0.01" "lcd.10NN.qt.0.05"
[387] "lcd.10NN.qt.0.95" "lcd.10NN.qt.0.99"
[389] "lcd.15NN.qt.0.01" "lcd.15NN.qt.0.05"
[391] "lcd.15NN.qt.0.95" "lcd.15NN.qt.0.99"
[393] "lcd.20NN.qt.0.01" "lcd.20NN.qt.0.05"
[395] "lcd.20NN.qt.0.95" "lcd.20NN.qt.0.99"
>
>
>
>
>
> dev.off()
null device
1
>