Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
Plots the coefficient of variation for different replicatesDescriptionThis function plots the coefficient of variation within replicates for a given value. If decoys are present these are removed before plotting. Usageplot_variation(data, column.values = "Intensity", Comparison = transition_group_id + Condition ~ BioReplicate, fun.aggregate = NULL, label=TRUE, ...) Arguments
ValueReturns a list with the data and calculated cv and a table that summarizes the mean, median and mode cv per Condition (if Condition is contained in the comparison). In addition it plots in Rconsole a violin plot with the observed coefficient of variations. Author(s)Peter Blattmann Examples
data("OpenSWATH_data", package="SWATH2stats")
data("Study_design", package="SWATH2stats")
data <- sample_annotation(OpenSWATH_data, Study_design)
plot_variation(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(SWATH2stats)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SWATH2stats/plot_variation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot_variation
> ### Title: Plots the coefficient of variation for different replicates
> ### Aliases: plot_variation
>
> ### ** Examples
>
> data("OpenSWATH_data", package="SWATH2stats")
> data("Study_design", package="SWATH2stats")
> data <- sample_annotation(OpenSWATH_data, Study_design)
> plot_variation(data)
[[1]]
transition_group_id
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2 101540_PLLHNFHSFLYQPDWVKR_3_run0
3 101541_PLLHNFHSFLYQPDWVKR_4_run0
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5 10187_GLGVEQLPVVFEDVVLHQATILPLAK_3_run0
6 10187_GLGVEQLPVVFEDVVLHQATILPLAK_3_run0
7 10188_GLGVEQLPVVFEDVVLHQATILPLAK_4_run0
8 10188_GLGVEQLPVVFEDVVLHQATILPLAK_4_run0
9 106133_DTYFDELR_2_run0
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13 106135_DTYFDRDVEELK_3_run0
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16 107313_DHPESPTPNPTEPLFLAQAEVYFLK_3_run0
17 107314_DHPESPTPNPTEPLFLAQAEVYFLK_4_run0
18 107314_DHPESPTPNPTEPLFLAQAEVYFLK_4_run0
19 107696_LQFGAQGSPFLFLK_2_run0
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27 108828_GNEQVTGLR_2_run0
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30 109325_LGMLSPEGTC(UniMod:4)K_2_run0
31 109326_LGM(UniMod:35)LSPEGTC(UniMod:4)K_2_run0
32 109326_LGM(UniMod:35)LSPEGTC(UniMod:4)K_2_run0
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36 110396_LSGIDANPNALFPPVEFPAPHLR_4_run0
37 110397_LSGIDANPNALFPPVEFPAPHLR_5_run0
38 110397_LSGIDANPNALFPPVEFPAPHLR_5_run0
39 110876_DDMVAQAMILK_2_run0
40 110876_DDMVAQAMILK_2_run0
41 111090_FPYVELDLHSYDLGIENILR_3_run0
42 111090_FPYVELDLHSYDLGIENILR_3_run0
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332 185915_VISGGPYEYPTR_3_run0
333 185916_VITGAPYEYPTR_2_run0
334 185916_VITGAPYEYPTR_2_run0
335 185917_VITGAPYEYPTR_3_run0
336 185917_VITGAPYEYPTR_3_run0
337 186355_TQNLPNC(UniMod:4)QLISR_2_run0
338 186355_TQNLPNC(UniMod:4)QLISR_2_run0
339 187498_SAEYNVNNLVSPVLFQEALWHVPEHAVVLEIAPHALLQAVLSTK_5_run0
340 187498_SAEYNVNNLVSPVLFQEALWHVPEHAVVLEIAPHALLQAVLSTK_5_run0
341 188706_EAEAAHGTVTVTR_2_run0
342 188706_EAEAAHGTVTVTR_2_run0
343 188707_EAEAAHGTVTVTR_3_run0
344 188707_EAEAAHGTVTVTR_3_run0
345 190290_AAVDLIIAVK_2_run0
346 190290_AAVDLIIAVK_2_run0
347 193069_ATFGVDESNAEVK_2_run0
348 193069_ATFGVDESNAEVK_2_run0
349 193070_ATFGVDESNAEVK_3_run0
350 193070_ATFGVDESNAEVK_3_run0
351 193420_ITYTPSDGTQEVK_2_run0
352 193420_ITYTPSDGTQEVK_2_run0
353 193421_ITYTPSDGTQEVK_3_run0
354 193421_ITYTPSDGTQEVK_3_run0
355 194552_TTVGSAEFVK_2_run0
356 194552_TTVGSAEFVK_2_run0
357 194767_DPQELNGITGVR_2_run0
358 194767_DPQELNGITGVR_2_run0
359 198043_EALLPLLVK_2_run0
360 198043_EALLPLLVK_2_run0
361 198045_EALLPLKGLEELVR_3_run0
362 198045_EALLPLKGLEELVR_3_run0
363 198310_FPATGYLSIVWLVK_2_run0
364 198310_FPATGYLSIVWLVK_2_run0
365 19
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and