accepted.amplicons: List Of Amplicon Indices That Passed Filter Criteria

In AmpliconDuo: Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

Description

Returns the indices of those amplicons in an ampliconduo data frame, that passed the applied filter criteria (ampliconduo data frames are filtered using the filter.ampliconduo or filter.ampliconduo.set function).

Usage

accepted.amplicons(x)

Arguments

x	An ampliconduo data frame or a list of ampliconduo data frames.

Details

Calling this function on an ampliconduo data frame, or a list of the latter, returns the indices of amplicons that passed the applied filter criteria. For each ampliconduo data frame an integer vector is created, and if a list of ampliconduo data frames is supplied with x, these are pooled in a list. The returned indices correspond to the data originally used to generate the ampliconduo data frames (parameter A and B in the ampliconduo function call).

Value

If x is an ampliconduo data frame, an integer vector is returned.

In case x is a list of ampliconduo data frames, a list of integer vectors is returned, one for each data frame.

Author(s)

Anja Lange & Daniel Hoffmann

See Also

filter.ampliconduo and filter.ampliconduo.set

Examples

## load example data
data(amplicons)

## apply filter criteria
ampliconduos.f <- filter.ampliconduo.set(amplicons, q = 0.05)

## return a list with accepted amplicons
good.reads <- accepted.amplicons(ampliconduos.f)

AmpliconDuo documentation built on July 1, 2020, 10:21 p.m.