envHash2otu_table: Convert a sequence-sample hash (like ENV file) into an OTU...

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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 )

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.