envHash2otu_table {phyloseq} | R Documentation

## Convert a sequence-sample hash (like ENV file) into an OTU table.

### Description

Parses an ENV-file into a sparse matrix of species-by-sample, where each species-row has only one non-zero value. We call this sparse abundance table the trivial OTU table, where every sequence is treated as a separate species. If a phylogenetic tree is available, it can be submitted with this table as arguments to `tip_glom` to create an object with a non-trivial `otu_table`.

### Usage

    envHash2otu_table(tipSampleTable)

### Arguments

`tipSampleTable` | (Required). A two-column character table (matrix or data.frame), where each row specifies the sequence name and source sample, consistent with the env-file for the UniFrac server (http://bmf2.colorado.edu/unifrac/).

### Value

`otu_table`. A trivial OTU table where each sequence is treated as a separate OTU.

### References

http://bmf2.colorado.edu/unifrac/

### See Also

`import_env_file`

`tip_glom`

`otu_table`

### Examples

    #
    ## fakeSeqNameVec <- paste("seq_", 1:8, sep="")
    ## fakeSamNameVec <- c(rep("A", 4), rep("B", 4))
    ## fakeSeqAbunVec <- sample(1:50, 8, TRUE)
    ## test    <- cbind(fakeSeqNameVec, fakeSamNameVec, fakeSeqAbunVec)
    ## testotu <- envHash2otu_table( test )
    ## test    <- cbind(fakeSeqNameVec, fakeSamNameVec)
    ## testotu <- envHash2otu_table( test )

[Package phyloseq version 1.38.0 Index]