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phyloseq

extract-methods

Method extensions to extraction operator for phyloseq objects.

Description

See the documentation for the Extract generic, defined in the R base-package for the expected behavior.

Usage

## S4 method for signature 'otu_table,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'sample_data,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'taxonomyTable,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'XStringSet,character,ANY,ANY'
x[i]

Arguments

x

object from which to extract element(s) or in which to replace element(s).

i

indices specifying elements to extract or replace. Indices are numeric or character vectors or empty (missing) or NULL. Numeric values are coerced to integer as by as.integer (and hence truncated towards zero). Character vectors will be matched to the names of the object (or for matrices/arrays, the dimnames): see ‘Character indices’ below for further details.

For [-indexing only: i, j, ... can be logical vectors, indicating elements/slices to select. Such vectors are recycled if necessary to match the corresponding extent. i, j, ... can also be negative integers, indicating elements/slices to leave out of the selection.

When indexing arrays by [ a single argument i can be a matrix with as many columns as there are dimensions of x; the result is then a vector with elements corresponding to the sets of indices in each row of i.

An index value of NULL is treated as if it were integer(0).

j

See Extract
...

See Extract
drop

For matrices and arrays. If TRUE the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement. See drop for further details.

Details

One special exception to standard behavior of these methods in phyloseq is that the drop argument is set internally to FALSE. This helps avoid bugs during complicated subsetting with multiple components, where it is necessary to be able to use a two dimensional indexing even if one of those dimensions has only 1 rank. Put another way, these phyloseq-defined extractions never collapse their result into a vector. See the documentation of Extract for more information about the drop argument.

See Also

Examples

data(esophagus)
nrow(otu_table(esophagus))
nrow(otu_table(esophagus)[1:5, ])
phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0
AGPL-3
Authors
Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain
Initial release
2019-04-23

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