ex: ExpressionSet instance for illustrating integrative smlSet...

In GGtools: software and data for analyses in genetics of gene expression

Description

ExpressionSet instance for illustrating integrative smlSet container

Usage

data(eset)

Format

The format is: 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: 0x10bf12948>
..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 7 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr [1:7] "hapmap family id" "hapmap person id" "id of mother of this person" "id of father of this person" ...
.. .. ..@ data :'data.frame': 90 obs. of 7 variables:
.. .. .. ..$ famid : int [1:90] 1341 1341 1341 1340 1340 1340 1340 1340 1341 1341 ...
.. .. .. ..$ persid : int [1:90] 14 2 13 9 10 2 11 1 11 1 ...
.. .. .. ..$ mothid : int [1:90] 0 14 0 0 0 12 0 10 0 12 ...
.. .. .. ..$ fathid : int [1:90] 0 13 0 0 0 11 0 9 0 11 ...
.. .. .. ..$ sampid : Factor w/ 90 levels "NA06985","NA06991",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. ..$ isFounder: logi [1:90] TRUE FALSE TRUE TRUE TRUE FALSE ...
.. .. .. ..$ male : logi [1:90] FALSE FALSE TRUE TRUE FALSE FALSE ...
.. .. ..@ 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': 0 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr(0)
.. .. ..@ data :'data.frame': 47293 obs. of 0 variables
.. .. ..@ 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 "illuminaHumanv1.db"
..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr(0)
.. .. ..@ data :'data.frame': 90 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] 2 14 0
.. .. .. ..$ : int [1:3] 2 13 7
.. .. .. ..$ : int [1:3] 1 3 0
.. .. .. ..$ : int [1:3] 1 0 0

Details

Expression data harvested in 2007 from GENEVAR

ftp://ftp.sanger.ac.uk/pub/genevar/CEU_parents_norm_march2007.zip

Examples

data(eset) # yields ExpressionSet instance called ex

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.