The directory path were the datafile are located. This is the current directory by default.
otufile
The OTU file. The only format currently supported is the Mothur format for .list files.
level
The OTU clustering level. By default this is 0.03. This level must correspond to levels present in the otufile.
fastafile
The fasta file. This is read in by ShortRead.
qualfile
The quality file. This is read in by ShortRead.
samplefile
The sample file. Currently this must be in Mothur format (.groups).
sampleADF
The sample meta data file. This is in AnnotatedDataFrame format.
assignmentADF
The assignment meta data file (the OTU meta data). This is generally in AnnotatedDataFrame format although it is also possible to read in an RDP classification file if there is only one read classification for each cluster and rdp=TRUE.
sADF.names
The column of the sampleADF file that has the sample names.
aADF.names
The column of the assignmentADF file that has the assignment names.
rdp
By default this is FALSE. Change to TRUE if assignmentADF is an RDP classification file. The RDP file must be in the fixed format.
otufiletype
The type of OTU file. Takes values "mothur", "cdhit", and "blastclust". Defaults to "mothur".
Examples
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")
soginOTU
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/readOTUset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readOTUset
> ### Title: readOTUset
> ### Aliases: readOTUset
>
> ### ** Examples
>
>
> 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
>
> soginOTU
Class: OTUsetF
Number of Sequences: 1000 reads
Sequence Width: 56..100 cycles
Number of OTUs: 399
Number of Samples: 8
sampleData: T ncol: 6
assignmentData: F
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.