Convert a sequence-sample hash (like ENV file) into an OTU table.
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.
envHash2otu_table(tipSampleTable)
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/). |
otu_table. A trivial OTU table where each sequence
is treated as a separate OTU.
#
## 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 )Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.