Last data update: 2014.03.03
|
R: subsetPeptideData
subsetPeptideData | R Documentation |
subsetPeptideData
Description
Given a matrix of peptide data, omit columns with excess missing data, specified by NAs.
Usage
subsetPeptideData(pepdat, numNAsAllowed = NULL, percentageNAsAllowed = 0.05)
Arguments
pepdat |
The peptide matrix, with peptides in columns and samples in rows.
|
numNAsAllowed |
The maximum count of missing values for each peptide (counts NAs).
|
percentageNAsAllowed |
The percentage of missing data allowed for each peptide over samples.
|
Value
Returns a matrix.
Author(s)
David L Gibbs
Examples
data(ProCoNA_Data)
subsetPeptideData(peptideData, percentageNAsAllowed=0.2)
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(ProCoNA)
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster
Attaching package: 'fastcluster'
The following object is masked from 'package:stats':
hclust
==========================================================================
*
* Package WGCNA 1.51 loaded.
*
* Important note: It appears that your system supports multi-threading,
* but it is not enabled within WGCNA in R.
* To allow multi-threading within WGCNA with all available cores, use
*
* allowWGCNAThreads()
*
* within R. Use disableWGCNAThreads() to disable threading if necessary.
* Alternatively, set the following environment variable on your system:
*
* ALLOW_WGCNA_THREADS=<number_of_processors>
*
* for example
*
* ALLOW_WGCNA_THREADS=4
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=4
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
Attaching package: 'WGCNA'
The following object is masked from 'package:stats':
cor
Loading required package: MSnbase
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: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics
This is MSnbase version 1.20.7
Read '?MSnbase' and references therein for information
about the package and how to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
Loading required package: flashClust
Attaching package: 'flashClust'
The following object is masked from 'package:fastcluster':
hclust
The following object is masked from 'package:stats':
hclust
Attaching package: 'ProCoNA'
The following object is masked from 'package:ProtGenerics':
peptides
The following object is masked from 'package:Biobase':
samples
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ProCoNA/subsetPeptideData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: subsetPeptideData
> ### Title: subsetPeptideData
> ### Aliases: subsetPeptideData
>
> ### ** Examples
>
> data(ProCoNA_Data)
> subsetPeptideData(peptideData, percentageNAsAllowed=0.2)
Removing peptides with more than 12 missing data points
33699225 7393735 191136635 7786631 83228277 7639507
1 1.60617707 -0.29566480 1.36314914 1.92324944 1.50575048 -1.390401718
2 -0.10852941 -1.33978948 -0.38302267 -0.47104963 -0.38690661 1.089973341
3 1.10879174 0.80262262 0.12399070 0.59175396 0.61513655 0.862103370
4 -0.20470465 0.13374983 -0.72927564 1.00270676 1.96011733 -0.573620646
5 -0.24032924 -0.47443430 0.27245834 0.07977294 0.69425909 0.051934904
6 0.72609948 0.36645343 -0.95367055 -1.36753154 0.65560457 -1.465597827
7 -1.45317618 -1.36111983 1.23103862 -0.82153182 -1.36813791 -0.210286368
8 0.06470469 -2.44214055 1.38165102 0.25093963 0.59561797 0.837802446
9 -0.05176296 1.06370310 -0.63095066 -2.44047463 1.27771385 0.207384113
10 1.14210132 -1.55967600 -0.16380802 -1.44776938 1.26551828 -0.082687429
11 1.81547405 -0.11993350 0.70501563 -0.77241324 -0.55512931 2.032694124
12 0.50204655 0.42474634 0.29688762 -0.43599906 -0.46612730 -0.554773380
13 -1.02628208 0.64712325 -1.32063098 0.78840810 -1.07788515 -0.439974286
14 -1.36184221 -1.36514922 0.36088166 0.39898253 1.10024881 -1.100032181
15 1.45440432 1.22441269 -0.14017497 -0.20386905 -0.38265770 0.356875269
16 1.22820101 -1.11604838 -0.24569477 0.34275464 -0.42409383 -0.793123066
17 0.79839848 0.39952321 0.73629089 -1.46360872 0.20046372 0.258794173
18 -1.16677071 1.36730335 1.05652354 -0.57487926 0.78829514 0.048941253
19 -0.71657672 -0.04617319 -0.51206533 0.24025799 -1.33929593 0.566288612
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21 -0.08906407 0.43484536 0.70905088 1.17179992 0.24534054 0.002347015
22 0.13047535 -1.59652280 -0.53344221 -0.65954445 -1.13934534 -0.428247412
23 0.14923299 1.20072214 0.27466458 0.84343630 -0.65101380 0.825009060
24 1.37687146 0.85368397 -0.03494946 0.97208304 -1.08495335 0.538941462
25 0.08740910 -0.55121878 -0.16227145 0.87439478 0.14435338 0.634429896
26 2.52821227 -0.79122637 -0.25273851 0.70625146 0.08990765 0.208851743
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31 -0.76828805 0.73366862 -1.22799846 -0.52269487 1.88351103 1.112971092
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33 -0.65215291 -0.80104723 -1.22596281 -1.42143827 -0.41289500 -1.544629601
34 -0.99817786 0.25246109 1.29811793 1.50565356 -1.01903475 0.017058563
35 0.50452683 2.73730341 0.30116898 -0.92669417 -0.60303628 -1.827424290
36 0.35751615 -0.26158928 1.30006101 -0.37219187 -0.20071573 0.817635213
37 0.29433066 0.12679141 0.88410517 0.97183229 -0.92917540 0.811440718
38 0.32875889 0.16263495 -0.62039096 0.86495111 -2.19766704 1.942132224
39 -2.45498480 -0.77295114 -0.12507430 -0.82556106 0.01341721 -0.340371689
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47 0.56574080 -0.29154749 1.61989851 1.78072256 0.05768928 -1.627067581
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50 0.43051552 0.24931343 -0.35771723 0.20702613 0.83070592 -0.441657214
51 0.10505463 -0.16994951 0.36170518 -0.80460404 -0.52039980 1.399738806
52 -0.23468181 -0.21593482 -0.46007345 0.64051718 1.05995831 0.481318060
53 0.81177015 -0.10956775 1.48350974 0.85003371 -1.68002666 1.099438718
54 0.18347147 -1.19909571 -1.77601129 -0.12969734 -0.79238786 -1.740424911
55 -1.37292524 -0.35566425 0.61464941 -1.66746770 1.56757921 0.707324837
56 -0.73832822 -2.09235429 -0.93923051 0.66636456 -0.20654770 0.109175706
57 1.02377165 0.07656756 -1.95699295 0.39118374 0.50002258 0.401875193
58 1.11555095 1.35165891 1.14185264 0.88046364 0.67125173 0.102661021
59 1.32375743 1.02902235 -2.00446745 -2.29913233 -0.04163643 -1.371665106
60 -0.17640811 1.11129190 1.53274177 -1.50261639 0.87552169 0.301662469
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2 -1.48220684 -1.71246145 -2.29521102 -1.11728208 -4.06642749 -1.90952501
3 -2.26664744 -1.37103910 -1.22272517 -2.27840687 -0.67122987 -0.92927001
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5 -0.45707369 -0.51445232 0.49332100 0.31096520 0.02427666 -0.17189586
6 -1.67397191 -0.71146497 -0.42427186 -2.11930446 -0.40133578 -0.61886662
7 0.38116408 0.07359050 1.13337080 -0.33290497 -0.76056787 0.74936899
8 0.02511237 0.01462434 -0.61389235 0.07377793 -0.58999517 -0.44980745
9 -0.75788462 0.33206963 0.23414470 0.38760355 -0.28318523 -0.19858159
10 0.62828992 1.90761955 0.77446378 0.66856832 0.51140867 0.39704038
11 0.98968393 0.36857118 -0.11518062 0.53886253 0.70688563 0.13807633
12 1.07072581 1.24199121 0.52010088 1.31296148 1.97978914 1.07540926
13 0.06805709 -0.25426828 -0.68798602 -0.58391602 -0.05777902 -0.02473707
14 0.01375371 0.08381666 -0.81844271 -1.03432048 0.57428115 0.06368869
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32 1.24773792 -0.38752637 -0.02770435 1.27633468 0.58596401 1.11535068
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35 1.57377045 1.19952756 -0.09374970 -0.35296400 0.70508863 0.49623594
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37 0.41199857 0.07669914 0.90370159 0.11593241 1.62264436 -1.16685054
38 0.93394602 1.78930438 1.14320986 2.14687019 1.64378863 2.11264936
39 1.77504044 0.42018834 0.81838925 0.72476732 1.42327596 1.00620911
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47 1.51448952 1.54334976 0.48949226 1.85159588 1.21100431 1.88313001
48 0.95854545 0.38313564 1.55760603 1.33644317 0.15284646 1.27434343
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56 0.05847603 0.24729582 0.42041415 -0.49180321 -0.41469926 1.09760594
57 1.32790004 0.01194511 1.36501542 1.37165836 1.60373554 1.27235047
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60 -0.74679792 -1.45278127 -0.02565235 0.34167788 0.82637139 0.00234299
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4 0.437529656 0.23678293 -0.688598972 -0.34483111 -0.77684825 -0.304259762
5 0.337151880 0.94732257 -0.814730882 0.01653736 0.62486998 0.965836744
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7 1.668957932 0.10942831 0.241080839 0.85127527 0.93738443 1.056146661
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33 -0.321338071 -0.61410218 0.312446904 -0.78602857 0.12281407 -0.353375007
34 0.872864886 1.08837991 0.639166641 1.10342033 1.00247351 -0.065527369
35 0.092627929 1.37570028 -0.572544679 0.51257444 0.07486762 1.159750401
36 -1.035781019 -0.70972007 -0.184185428 0.69559685 -0.87165191 -0.157140852
37 0.425980581 1.40974827 1.062815465 0.50505194 -0.51463186 0.255577349
38 1.403343874 1.64676134 2.023850239 0.85812120 1.60277887 1.427813838
39 1.259443627 0.58780622 0.726097144 0.14052409 1.05288826 0.005376822
40 0.692588142 -0.19777284 -0.647955415 -0.47406644 0.16176345 -1.359272068
41 0.107753931 0.09702567 -0.114450737 0.22467962 0.11965383 0.801663533
42 0.215718693 -0.33360453 -0.828510433 -0.70544863 -0.58733835 -1.554961643
43 1.857794400 -0.60139082 0.626756640 1.91196236 0.57968862 0.136877997
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45 -0.300853903 -0.68942567 -0.588530688 0.03557745 0.33519574 -0.896565659
46 0.737458192 0.25485516 -0.462300569 0.68969914 -0.33609530 -1.070267690
47 2.064741062 1.60613688 2.695577307 1.01382100 1.61837133 1.442578324
48 0.986680617 0.08272651 1.263146328 -0.30421191 1.24192021 0.133329835
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|