mergeSequenceTables {dada2} | R Documentation

## Merge two or more sample-by-sequence observation matrices.

### Description

This function combines sequence tables together into one merged sequences table.

### Usage

    mergeSequenceTables(table1 = NULL, table2 = NULL, ..., tables = NULL,
      repeats = "error", orderBy = "abundance")

### Arguments

`table1` | (Optional, default=NULL). Named integer matrix. Rownames correspond to samples and column names correspond to sequences. The output of `makeSequenceTable`.
`table2` | (Optional, default=NULL). Named integer matrix. Rownames correspond to samples and column names correspond to sequences. The output of `makeSequenceTable`.
`...` | (Optional). Additional sequence tables.
`tables` | (Optional, default=NULL). Either a list of sequence tables, or a list/vector of RDS filenames corresponding to sequence tables. If provided, `table1`, `table2`, and any additional arguments will be ignored.
`repeats` | (Optional). Default "error". Specifies how merging should proceed in the presence of repeated sample names. Valid values: "error", "sum". If "sum", then samples with the same name are summed together in the merged 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 unwieldy.

### See Also

`makeSequenceTable`

### Examples

    ## Not run:
      mergetab <- mergeSequenceTables(seqtab1, seqtab2, seqtab3) # unnamed arguments are assumed to be individual sequence tables
      input_tables <- list(seqtab1, seqtab2, seqtab3)
      mergetab <- mergeSequenceTables(tables=input_tables) # list of sequence tables
      files <- c(file1, file2, file3)
      mergetab <- mergeSequenceTables(tables=files) # vector of filenames

    ## End(Not run)

[Package dada2 version 1.10.1 Index]