These are other functions available. Caution is advised when using them. Some are still in development and others only work on specific objects (OTUset or TAXset).
The column of the sampleData or assignmentData dataframe that contains the value.
value
The desired value.
exact
If exact=T value must match perfectly. If exact=F value will grep instead of match.
...
Other arguments. Often these are passed to abundance
Details
getOTUs Returns OTU names that match given values in the assignmentData dataframe.
getSamples Returns sample names that match given values in the sampleData dataframe.
o_diversity Wrapper for vegan's diversity function.
o_estimateR Wrapper for vegan's estimateR function.
otuseqplot Plots the samples acording to number of OTUs and number of sequences.
otusize Returns the size of each OTU.
otuspersample Lists the number of OTUs in each sample.
rseqplot Plots the samples by estimated richness and number of sequences.
seqspersample Returns the number of sequences in each sample.
sharedotus Returns the number of OTUs shared between samples.
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")
getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE)
o_estimateR(soginOTU)
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.
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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(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/other_functions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: other_functions
> ### Title: Other functions
> ### Aliases: getOTUs getSamples o_diversity o_estimateR otuseqplot otusize
> ### otuspersample rseqplot seqspersample sharedotus
>
> ### ** 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
>
> getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE)
[1] "53R" "137" "138"
>
> o_estimateR(soginOTU)
s
112R 115R 137 138 53R 55R
S.obs 57.000000 44.000000 49.000000 48.00000 37.000000 29.000000
S.chao1 192.125000 176.000000 254.000000 159.42857 145.750000 191.500000
se.chao1 60.975679 74.630319 110.794024 53.88188 62.860021 104.644533
S.ACE 283.067602 154.791782 230.006548 320.32000 147.625000 182.685606
se.ACE 7.841178 8.026768 5.532269 11.21429 3.619804 2.553564
s
FS312 FS396
S.obs 110.00000 130.00000
S.chao1 384.61538 308.00000
se.chao1 96.01630 54.70480
S.ACE 579.22305 392.65701
se.ACE 16.82521 12.75554
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.