mergeSequenceTables: Merge two or more sample-by-sequence observation matrices.

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

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",
  tryRC = FALSE
)

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.
tryRC	(Optional). logical(1). Default FALSE. If tryRC=TRUE, sequences whose reverse complement matches an earlier sequence will be reverse- complemented and merged together with that earlier sequence. This is most useful when different runs sequenced the same gene region in different or mixed orientations. Note, this does not guarantee consistent orientatation from e.g. 5' to 3' on the gene, it just ensures that identical sequences in different orientations are merged.

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 assumed to be 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)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.