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Last data update: 2014.03.03

R: AmpliconDuo Amplicon Filter

filter.ampliconduo

R Documentation

AmpliconDuo Amplicon Filter

Description

Marks or removes amplicons from an ampliconduo data frame according to the specified filter criteria.

Usage

filter.ampliconduo(x, min.freq = 1, OR = NULL, q = NULL, p = NULL, remove = FALSE)

Arguments

`x`	Data frame, an ampliconduo data frame returned by the `ampliconduo` function.
`min.freq`	Optional. Integer, minimium frequency/read count for an amplicon in each of the two amplicon sets to be retained. Default value is 1.
`OR`	Optional. Numeric, minimum odds ratio for an amplicon to be retained. If no value is specified the odds ratio is excluded from the filter criteria.
`q`	Optional. Numeric, minimum value for `q`, the adjusted p-value for an amplicon to pass the filter. If no value is specified, `q` is excluded from the filter criteria.
`p`	Optional. Numeric, minimum p-value for an amplicon to pass the filter. If no value for `p` is specified `p` is excluded from the filter criteria.
`remove`	Optional. Logical, decides whether amplicons that fail the filter criteria should be removed (`TRUE`), or retained (`FALSE`).

Details

Takes the ampliconduo data frame x and applies each filter criterion that is selected to each amplicon. If an amplicon i does not pass each of the applied criteria, the logical value in column rejected in row i is set to TRUE. In case the parameter remove was set to TRUE, all amplicons with rejected = TRUE are removed. The position information with respect to the data used as input for the ampliconduo call is retained.

Value

Data frame corresponding to the input x, but with the adjustments in the rejected column according to the specified filter criteria, or removed rows (removed = TRUE).

Author(s)

Anja Lange & Daniel Hoffmann

Examples

##load example data
data(amplicons)

## extract the first ampliconduo data frame
ampliconduo1 <- amplicons[[1]]

## apply filter criteria 
ampliconduo1.f <- filter.ampliconduo(ampliconduo1)
ampliconduo1.f <- filter.ampliconduo(ampliconduo1, min.freq = 2, remove = TRUE)

## to return a list with the indices (corresponding to the indices of the data 
## the ampliconduo function was called on) of all amplicons that passed the filter criteria 
good.reads <- accepted.amplicons(ampliconduo1.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
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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/filter.ampliconduo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filter.ampliconduo
> ### Title: AmpliconDuo Amplicon Filter
> ### Aliases: filter.ampliconduo
> ### Keywords: manip
> 
> ### ** Examples
> 
> ##load example data
> data(amplicons)
> 
> ## extract the first ampliconduo data frame
> ampliconduo1 <- amplicons[[1]]
> 
> ## apply filter criteria 
> ampliconduo1.f <- filter.ampliconduo(ampliconduo1)
> ampliconduo1.f <- filter.ampliconduo(ampliconduo1, min.freq = 2, remove = TRUE)
> 
> ## to return a list with the indices (corresponding to the indices of the data 
> ## the ampliconduo function was called on) of all amplicons that passed the filter criteria 
> good.reads <- accepted.amplicons(ampliconduo1.f)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>