makeSequenceTable {dada2} | R Documentation

## Construct a sample-by-sequence observation matrix.

### Description

This function constructs a sequence table (analogous to an OTU table) from the provided list of samples.

### Usage

    makeSequenceTable(samples, orderBy = "abundance")

### Arguments

`samples` | (Required). A `list` of the samples to include in the sequence table. Samples can be provided in any format that can be processed by `getUniques`. Sample names are propagated to the rownames of the sequence table.
`orderBy` | (Optional). `character(1)`. Default "abundance". Specifies how the sequences (columns) of the returned table should be ordered (decreasing). Valid values: "abundance", "nsamples", NULL.

### Value

Named integer matrix. A row for each sample, and a column for each unique sequence across all the samples. Note that the columns are named by the sequence which can make display a little unwieldy.

### See Also

`dada`, `getUniques`

### Examples

    derep1 <- derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
    derep2 <- derepFastq(system.file("extdata", "sam2F.fastq.gz", package="dada2"))
    dada1 <- dada(derep1, tperr1)
    dada2 <- dada(derep2, tperr1)
    makeSequenceTable(list(sample1=dada1, sample2=dada2))

[Package dada2 version 1.10.1 Index]