do_track_dada2: Construct Sequence Table, Remove Chimeras, and Assign...

Description Usage Arguments Value References Examples

Description

Construct Sequence Table, Remove Chimeras, and Assign Taxonomy

Usage

1
do_track_dada2(out, dadaFs, mergers, seqtab, seqtab_nochim, sample_names)

Arguments

out

matrix output from 'filterAndTrim()' function

dadaFs

dada object output from 'dada()' function for forward reads

mergers

output from 'mergePairs()' function

seqtab

sequence table output from 'makeSequenceTable()'

seqtab_nochim

output from 'removeBimeraDenovo()'

sample_names

vector of sample names

Value

matrix of sample rows and metric columns over the previous pipeline steps

References

See "Track Reads Through the Pipeline" http://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline

Examples

1
2
do_track_dada2(out, dadaFs, getN, mergers, seqtab, seqtab_nochim,
sample_names)

erictleung/dada2HPCPipe documentation built on May 10, 2019, 1:19 p.m.