Position-dependent Gene Expression

Description

An ExpressionSet object containing single-cell gene expression measured by qPCR, with cells facing the blastocyst cavity labelled fluorescently.

Usage

data(xql)

Format

Formal class 'ExpressionSet' [package "Biobase"] with 7 slots
  ..@ experimentData   :Formal class 'MIAME' [package "Biobase"] with 13 slots
  .. .. ..@ name             : chr ""
  .. .. ..@ lab              : chr ""
  .. .. ..@ contact          : chr ""
  .. .. ..@ title            : chr ""
  .. .. ..@ abstract         : chr ""
  .. .. ..@ url              : chr ""
  .. .. ..@ pubMedIds        : chr ""
  .. .. ..@ samples          : list()
  .. .. ..@ hybridizations   : list()
  .. .. ..@ normControls     : list()
  .. .. ..@ preprocessing    : list()
  .. .. ..@ other            : list()
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. .. .. ..@ .Data:List of 2
  .. .. .. .. .. ..$ : int [1:3] 1 0 0
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ assayData        :<environment: 0x7fe9c10> 
  ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':  2 obs. of  1 variable:
  .. .. .. ..$ labelDescription: chr [1:2] NA NA
  .. .. ..@ data             :'data.frame':	43 obs. of  2 variables:
  .. .. .. ..$ Embryonic.day: chr [1:43] "E4.5" "E4.5" "E4.5" "E4.5" ...
  .. .. .. ..$ Label        : chr [1:43] "High" "High" "Low" "Low" ...
  .. .. ..@ dimLabels        : chr [1:2] "sampleNames" "sampleColumns"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ featureData      :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':	1 obs. of  1 variable:
  .. .. .. ..$ labelDescription: chr NA
  .. .. ..@ data             :'data.frame':	10 obs. of  1 variable:
  .. .. .. ..$ symbol: chr [1:10] "Fgf4" "Cubn" "Sox17" "Lama1" ...
  .. .. ..@ dimLabels        : chr [1:2] "featureNames" "featureColumns"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ annotation       : chr "single cell qPCR"
  ..@ protocolData     :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
  .. .. ..@ varMetadata      :'data.frame':	0 obs. of  1 variable:
  .. .. .. ..$ labelDescription: chr(0) 
  .. .. ..@ data             :'data.frame':	43 obs. of  0 variables
  .. .. ..@ dimLabels        : chr [1:2] "sampleNames" "sampleColumns"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 1 1 0
  ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
  .. .. ..@ .Data:List of 4
  .. .. .. ..$ : int [1:3] 3 0 1
  .. .. .. ..$ : int [1:3] 2 20 1
  .. .. .. ..$ : int [1:3] 1 3 0
  .. .. .. ..$ : int [1:3] 1 0 0

References

Ohnishi et al., 2014

See Also

a, x, xq

Examples

data(xql)
xql
pData(xql)

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(Hiiragi2013)
Loading required package: affy
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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
Loading required package: lattice

Attaching package: 'lattice'

The following object is masked from 'package:boot':

    melanoma

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 objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools

Attaching package: 'gtools'

The following objects are masked from 'package:boot':

    inv.logit, logit

Loading required package: KEGGREST
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

The following object is masked from 'package:genefilter':

    area

Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db


Loading required package: RColorBrewer
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Hiiragi2013/xql.Rd_%03d_medium.png", width=480, height=480)
> ### Name: xql
> ### Title: Position-dependent Gene Expression
> ### Aliases: xql
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(xql)
> xql
ExpressionSet (storageMode: lockedEnvironment)
assayData: 10 features, 43 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: 0711_e4.5_1 0711_e4.5_2 ... 0512_e35_12 (43 total)
  varLabels: Embryonic.day Label
  varMetadata: labelDescription
featureData
  featureNames: Fgf4 Cubn ... Pdgfra (10 total)
  fvarLabels: symbol
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: single cell qPCR 
> pData(xql)
             Embryonic.day Label
0711_e4.5_1           E4.5  High
0711_e4.5_2           E4.5  High
0711_e4.5_5           E4.5   Low
0711_e4.5_6           E4.5   Low
0711_e4.5_7           E4.5   Low
0711_e4.5_8           E4.5   Low
0711_e4.5_9           E4.5   Low
2811_e4.5_1           E4.5  High
2811_e4.5_2           E4.5  High
2811_e4.5_3           E4.5  High
2811_e4.5_4           E4.5  High
2811_e4.5_5           E4.5  High
2811_e4.5_6           E4.5  High
2811_e4.5_7           E4.5  High
2811_e4.5_8           E4.5  High
2811_e4.5_9           E4.5  High
2811_e4.5_10          E4.5   Low
2811_e4.5_11          E4.5   Low
2811_e4.5_12          E4.5   Low
2811_e4.5_13          E4.5   Low
2211_e3.5_4           E3.5  High
2211_e3.5_8           E3.5   Low
2211_e3.5_9           E3.5   Low
2211_e3.5_10          E3.5   Low
2211_e3.5_11          E3.5   Low
2211_e3.5_12          E3.5   Low
3011_e3.5_1           E3.5  High
3011_e3.5_4           E3.5  High
3011_e3.5_6           E3.5  High
3011_e3.5_7           E3.5  High
3011_e3.5_8           E3.5   Low
3011_e3.5_9           E3.5   Low
0412_e3.5_1           E3.5  High
0412_e3.5_4           E3.5  High
0412_e3.5_5           E3.5  High
0412_e3.5_6           E3.5  High
0412_e3.5_13          E3.5   Low
2711_e3.5_4           E3.5   Low
0312_e3.5_3           E3.5  High
0312_e3.5_5           E3.5  High
0512_e35_6            E3.5   Low
0512_e35_9            E3.5   Low
0512_e35_12           E3.5   Low
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>