Supported by Dr. Osamu Ogasawara and  providing  . |
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Last data update: 2014.03.03 |
abundanceDescription
Usageabundance(object, ...) Arguments
DetailsThese are other arguments passed to
ValueThe returned value will be a data.frame. Examples
## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")
## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")
## calculate abundance
abundance(soginOTU, collab="Site")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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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
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> library(OTUbase)
Loading required package: S4Vectors
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
================================================================================
Welcome to OTUbase version 1.22.0
Attaching package: 'OTUbase'
The following object is masked from 'package:GenomicAlignments':
seqnames
The following object is masked from 'package:SummarizedExperiment':
seqnames
The following object is masked from 'package:GenomicRanges':
seqnames
The following object is masked from 'package:GenomeInfoDb':
seqnames
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OTUbase/abundance.Rd_%03d_medium.png", width=480, height=480)
> ### Name: abundance
> ### Title: abundance
> ### Aliases: abundance,.TAXset-method abundance,.OTUset-method abundance
> ### Keywords: abundance
>
> ### ** Examples
>
>
> ## locate directory with data
> dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")
>
> ## read in data into OTUset object
> soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")
Looking for column with names
>
> ## calculate abundance
> abundance(soginOTU, collab="Site")
s
o Lower deep water Oxygen minimum Labrador seawater Labrador seawater
otu1 0 0 2 1
otu10 2 0 0 0
otu100 1 0 0 0
otu101 0 0 0 0
otu102 0 0 0 1
otu103 0 0 0 0
otu104 0 0 0 0
otu105 1 0 0 1
otu106 0 1 0 1
otu107 0 0 1 0
otu108 0 0 1 0
otu109 0 0 0 1
otu11 0 0 0 1
otu110 0 0 1 0
otu111 1 0 0 0
otu112 1 0 0 0
otu113 1 0 0 0
otu114 0 0 0 0
otu115 1 0 0 0
otu116 0 1 0 0
otu117 0 0 0 1
otu118 0 0 0 0
otu119 0 0 0 0
otu12 0 4 2 0
otu120 0 0 0 0
otu121 0 1 0 0
otu122 0 0 0 0
otu123 0 0 0 0
otu124 0 0 0 0
otu125 0 0 0 0
otu126 0 0 1 0
otu127 0 0 0 0
otu128 0 0 0 0
otu129 0 0 0 0
otu13 0 0 0 0
otu130 0 0 0 0
otu131 0 0 0 0
otu132 0 0 0 0
otu133 0 0 0 0
otu134 0 0 0 0
otu135 0 0 0 0
otu136 0 0 0 0
otu137 0 0 0 0
otu138 0 1 3 2
otu139 0 0 0 0
otu14 1 6 5 9
otu140 0 0 0 0
otu141 0 0 0 0
otu142 0 0 1 0
otu143 0 0 1 0
otu144 0 0 0 1
otu145 0 0 0 0
otu146 0 0 0 1
otu147 0 0 0 1
otu148 0 0 0 0
otu149 0 1 0 0
otu15 0 0 0 0
otu150 0 0 0 0
otu151 0 0 0 0
otu152 0 0 1 0
otu153 1 0 0 0
otu154 0 0 0 0
otu155 0 0 0 0
otu156 0 0 0 0
otu157 0 1 0 0
otu158 1 0 0 0
otu159 0 0 0 1
otu16 0 0 1 0
otu160 0 0 0 0
otu161 0 0 0 0
otu162 0 0 0 0
otu163 0 0 0 0
otu164 0 0 0 0
otu165 0 0 0 0
otu166 0 0 0 0
otu167 0 0 0 0
otu168 0 0 0 0
otu169 0 0 0 0
otu17 0 0 0 1
otu170 0 0 0 0
otu171 0 0 0 0
otu172 0 0 0 0
otu173 0 0 0 0
otu174 0 0 0 0
otu175 0 0 0 0
otu176 0 0 0 0
otu177 0 0 0 0
otu178 0 0 0 0
otu179 0 0 0 0
otu18 2 1 0 0
otu180 0 0 0 0
otu181 0 0 0 0
otu182 0 0 0 0
otu183 0 0 0 0
otu184 0 0 0 0
otu185 0 0 0 0
otu186 0 0 0 0
otu187 0 0 0 0
otu188 0 0 0 0
otu189 0 0 0 0
otu19 0 0 1 0
otu190 0 0 0 0
otu191 0 0 0 0
otu192 0 0 0 0
otu193 0 0 0 0
otu194 0 0 0 0
otu195 0 0 0 0
otu196 0 0 0 0
otu197 0 0 0 0
otu198 0 0 0 0
otu199 0 0 0 0
otu2 0 0 0 1
otu20 1 1 0 1
otu200 0 0 0 0
otu201 0 0 0 0
otu202 0 0 0 0
otu203 0 0 0 0
otu204 0 0 0 0
otu205 0 0 1 0
otu206 1 0 0 0
otu207 0 0 0 1
otu208 1 0 0 0
otu209 1 0 0 0
otu21 0 2 0 0
otu210 0 0 0 0
otu211 0 0 0 0
otu212 0 0 1 0
otu213 0 0 0 0
otu214 0 0 1 0
otu215 0 0 0 0
otu216 0 1 0 0
otu217 0 0 0 0
otu218 0 0 1 0
otu219 0 0 0 1
otu22 0 0 0 0
otu220 0 1 0 0
otu221 1 2 0 0
otu222 0 0 0 0
otu223 0 0 1 0
otu224 0 0 2 0
otu225 0 0 0 0
otu226 0 1 0 0
otu227 0 0 0 0
otu228 0 0 0 0
otu229 1 0 0 0
otu23 0 0 0 0
otu230 1 0 0 0
otu231 0 0 0 0
otu232 0 0 0 1
otu233 0 0 0 2
otu234 3 0 1 0
otu235 0 0 0 0
otu236 0 0 0 0
otu237 0 0 0 0
otu238 0 0 0 0
otu239 2 0 0 0
otu24 0 0 0 0
otu240 0 1 0 0
otu241 0 0 0 0
otu242 2 1 0 0
otu243 1 0 0 0
otu244 0 0 1 0
otu245 0 1 1 0
otu246 0 0 0 1
otu247 0 0 0 1
otu248 0 1 0 0
otu249 0 0 1 0
otu25 0 0 0 0
otu250 1 0 0 0
otu251 4 0 0 0
otu252 0 3 1 1
otu253 1 0 0 0
otu254 0 0 0 0
otu255 0 0 0 0
otu256 0 0 0 0
otu257 0 0 0 0
otu258 0 0 0 0
otu259 0 0 0 0
otu26 0 1 0 0
otu260 0 0 0 1
otu261 0 0 0 0
otu262 0 0 0 0
otu263 0 0 0 0
otu264 0 0 0 0
otu265 0 0 0 0
otu266 0 0 0 0
otu267 0 0 0 0
otu268 0 0 0 0
otu269 0 0 0 0
otu27 0 0 1 0
otu270 0 0 0 0
otu271 0 0 0 0
otu272 0 1 0 0
otu273 0 0 0 0
otu274 0 0 0 0
otu275 0 1 0 0
otu276 0 0 0 1
otu277 0 0 0 1
otu278 2 3 0 0
otu279 0 0 1 1
otu28 0 0 0 0
otu280 0 0 1 0
otu281 0 0 0 0
otu282 0 0 0 0
otu283 0 0 0 0
otu284 0 0 0 0
otu285 0 0 0 0
otu286 0 0 0 0
otu287 0 0 0 0
otu288 0 0 0 0
otu289 0 0 0 0
otu29 0 0 0 0
otu290 1 0 0 0
otu291 1 0 0 0
otu292 1 0 0 0
otu293 0 0 0 0
otu294 0 0 0 0
otu295 0 0 0 0
otu296 0 0 0 0
otu297 0 0 0 0
otu298 0 0 0 0
otu299 0 0 0 0
otu3 0 0 0 0
otu30 0 0 0 0
otu300 0 0 0 0
otu301 0 0 0 0
otu302 0 0 0 0
otu303 0 0 0 0
otu304 0 0 0 0
otu305 1 0 0 0
otu306 2 0 0 0
otu307 0 1 0 0
otu308 1 0 0 0
otu309 0 0 1 0
otu31 0 0 0 0
otu310 0 0 0 0
otu311 0 0 0 0
otu312 0 0 0 0
otu313 0 1 1 0
otu314 0 0 0 0
otu315 0 0 0 0
otu316 0 0 0 0
otu317 0 0 0 0
otu318 0 0 0 0
otu319 0 0 0 0
otu32 0 0 0 0
otu320 0 0 0 0
otu321 1 0 0 0
otu322 0 0 0 0
otu323 0 0 0 0
otu324 0 0 0 0
otu325 0 0 0 0
otu326 0 0 0 0
otu327 1 0 0 0
otu328 1 0 0 0
otu329 0 0 0 0
otu33 1 0 0 0
otu330 0 0 0 0
otu331 0 0 0 0
otu332 0 0 0 0
otu333 0 0 0 0
otu334 0 0 0 0
otu335 0 0 0 1
otu336 0 0 0 0
otu337 0 1 0 0
otu338 0 1 0 0
otu339 1 0 0 0
otu34 0 0 1 0
otu340 2 0 0 0
otu341 0 0 0 0
otu342 0 0 0 0
otu343 0 0 0 0
otu344 0 0 0 0
otu345 0 0 0 0
otu346 0 0 0 0
otu347 0 0 0 0
otu348 0 0 0 0
otu349 0 0 0 0
otu35 0 0 1 0
otu350 0 0 0 0
otu351 0 0 0 0
otu352 0 0 0 0
otu353 0 0 0 0
otu354 0 0 0 0
otu355 0 1 0 0
otu356 0 0 0 0
otu357 0 0 0 0
otu358 0 1 0 0
otu359 0 0 0 1
otu36 1 0 0 0
otu360 0 0 0 0
otu361 0 0 0 0
otu362 0 1 1 0
otu363 0 0 1 2
otu364 7 4 1 0
otu365 0 0 0 1
otu366 1 0 0 0
otu367 0 0 0 0
otu368 0 0 0 0
otu369 0 0 0 0
otu37 0 0 0 0
otu370 1 0 0 1
otu371 1 0 0 0
otu372 0 0 0 0
otu373 1 0 0 0
otu374 0 0 0 0
otu375 0 0 0 0
otu376 0 0 0 1
otu377 0 0 0 1
otu378 0 0 0 0
otu379 0 0 0 0
otu38 0 0 0 2
otu380 0 0 0 0
otu381 0 0 0 0
otu382 0 0 0 0
otu383 0 0 0 0
otu384 0 0 0 0
otu385 0 0 0 0
otu386 0 4 0 2
otu387 0 0 0 0
otu388 0 0 0 1
otu389 1 9 5 4
otu39 1 3 0 1
otu390 0 0 0 1
otu391 0 0 0 1
otu392 0 0 0 0
otu393 0 1 0 0
otu394 0 0 1 0
otu395 0 2 3 1
otu396 0 0 0 1
otu397 0 1 0 0
otu398 0 0 0 0
otu399 1 0 0 0
otu4 1 0 0 0
otu40 0 0 0 0
otu41 0 1 1 0
otu42 1 0 0 0
otu43 1 0 0 1
otu44 0 0 0 0
otu45 0 0 0 0
otu46 0 0 0 0
otu47 0 0
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and