List Of Amplicon Indices That Passed Filter Criteria

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(AmpliconDuo)
Loading required package: ggplot2
Loading required package: xtable
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/AmpliconDuo/accepted.amplicons.Rd_%03d_medium.png", width=480, height=480)
> ### Name: accepted.amplicons
> ### Title: List Of Amplicon Indices That Passed Filter Criteria
> ### Aliases: accepted.amplicons
> ### Keywords: list
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>