This data contains MassArray spectral information for two samples.
Usage
MassArray.example.data
Format
The format is:
Formal class 'MassArrayData' [package "MassArray"] with 17 slots
..@ sequence : chr "CCAGGTCCAAAGGTTCAGACCAGTCTGAACCTGTCCAGGGGCACTCCATATTTTCCTACCTGTCCCTCTTTGCTTGTAAAAACAAATTAAACAGGGATCCCAGCAACTTCGGGGCATGTGTGTAACT"| __truncated__
..@ chr : chr(0)
..@ start : int(0)
..@ end : int(0)
..@ strand : chr "+"
..@ fwd.tag : chr "AGGAAGAGAG"
..@ rev.tag : chr "AGCCTTCTCCC"
..@ fwd.primer : num 29
..@ rev.primer : num 27
..@ lower.threshold : num 1500
..@ upper.threshold : num 9000
..@ fragments.T :List of 89
.. ..$ :Formal class 'MassArrayFragment' [package "MassArray"] with 21 slots
.. .. .. ..@ ID : int 1
.. .. .. ..@ assay.name : chr ""
.. .. .. ..@ name : chr ""
.. .. .. ..@ sequence : chr "GGGAGAAGGCT"
.. .. .. ..@ position : int 385
.. .. .. ..@ length : int 11
.. .. .. ..@ CpGs : int 0
.. .. .. ..@ MW : num 3913
.. .. .. ..@ collisions : int 0
.. .. .. ..@ collision.IDs :List of 1
.. .. .. .. ..$ : int(0)
.. .. .. ..@ CG.collisions : int 0
.. .. .. ..@ CG.collision.IDs : list()
.. .. .. ..@ type : chr "T"
.. .. .. ..@ direction : chr "+"
.. .. .. ..@ extra : chr "5PPP-3P"
.. .. .. ..@ bisulfite.converted: logi TRUE
.. .. .. ..@ assayable : logi TRUE
.. .. .. ..@ conversion.control : logi FALSE
.. .. .. ..@ required : logi FALSE
.. .. .. ..@ ignored : logi FALSE
.. .. .. ..@ primer : logi TRUE
..@ samples :List of 2
.. ..$ :Formal class 'MassArraySpectrum' [package "MassArray"] with 9 slots
.. .. .. ..@ sample : chr "A"
.. .. .. ..@ rxn : chr "T"
.. .. .. ..@ strand : chr "+"
.. .. .. ..@ peaks :List of 184
.. .. .. .. ..$ :Formal class 'MassArrayPeak' [package "MassArray"] with 16 slots
.. .. .. .. .. .. ..@ ID : int 1
.. .. .. .. .. .. ..@ MW.theoretical : num 1111
.. .. .. .. .. .. ..@ MW.actual : num NA
.. .. .. .. .. .. ..@ probability : num 0
.. .. .. .. .. .. ..@ SNR : num 0
.. .. .. .. .. .. ..@ height : num NA
.. .. .. .. .. .. ..@ sample.intensity: num NA
.. .. .. .. .. .. ..@ ref.intensity : num 0.1
.. .. .. .. .. .. ..@ sequence : chr "ACACAAT"
.. .. .. .. .. .. ..@ adduct : chr ""
.. .. .. .. .. .. ..@ type : chr "Modified"
.. .. .. .. .. .. ..@ charge : int 1
.. .. .. .. .. .. ..@ collisions : int 0
.. .. .. .. .. .. ..@ components : int 0
.. .. .. .. .. .. ..@ missing : logi TRUE
.. .. .. .. .. .. ..@ new : logi FALSE
.. .. .. ..@ quality.conversion : num [1:4] 0.0529 0 0 0
.. .. .. ..@ quality.spectra : num NA
.. .. .. ..@ quality.primerdimer: num [1:7] 8.51 15.83 3.28 1.04 0 ...
.. .. .. ..@ quality.contaminant: num NA
.. .. .. ..@ quality.adducts : num [1:114] 1 1 0.97 0.231 0.412 ...
..@ groups : chr(0)
..@ CpG.data : num [1:2, 1:18] 0.0322 0.0449 0.1468 0.3641 0.1468 ...
..@ CpG.data.combined: num [1:2, 1:18] 0.0322 0.0449 0.1468 0.3641 0.1468 ...
Source
Thompson et al. 2009
Examples
data(MassArray.example.data)
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(MassArray)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassArray/MassArray.example.data.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MassArray.example.data
> ### Title: MassArray Data object
> ### Aliases: MassArray.example.data
> ### Keywords: datasets
>
> ### ** Examples
>
> data(MassArray.example.data)
>
>
>
>
>
> dev.off()
null device
1
>