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Last data update: 2014.03.03

R: Measure Of Discordance Between Two Amplicon Data Sets

discordance.delta

R Documentation

Measure Of Discordance Between Two Amplicon Data Sets

Description

Calculates delta (Δ) and delta prime (Δ'), the fraction of amplicon frequencies and amplicons, respectively, with a false discovery rate below a certain threshold θ as a measure of discordance between two amplicon data sets A and B.

Usage

discordance.delta(x, names = NULL, theta = 0.05, corrected = TRUE,
printToTex = FALSE, directory = NULL, file.name = NULL)

Arguments

`x`	A list of amplicon duo data frames as returned by the `ampliconduo` function.
`names`	Optional. Vector or list of characters specifying the sample/amplicon pair names. By default names are taken from the element names of `x`.
`theta`	Optional. Numeric, threshold for the false discovery rate. Default value is 0.05.
`corrected`	Optional. Logical, indicates whether the p-value from Fisher's exact test (FALSE) or the adjusted p-value (TRUE), here called q, is used for calculation of Δ and Δ'.
`printToTex`	Optional. Logical, if `TRUE` writes a file with the resulting table in Tex format. Default is `FALSE`.
`directory`	Optional. If `printToTex` is `TRUE`, the output file will be saved in the specified directory.
`file.name`	Optional. If `printToTex` is `TRUE`, the output file will have the name `file.name`.

Details

Calculates Δ and Δ', the fraction of frequencies of amplicons and amplicons, respectively, with false discovery rate below a certain threshold θ as a measure of discordance between two amplicon data sets A and B with occurence r_{(iAS)} of amplicon i in amplicon set A of sample S (the ampliconduo data frame). Δ and Δ' are defined as follows:

for number n_S of amplicons detected in sample/ampliconduo S. Δ_{Sθ} and Δ'_{Sθ} are located between 0 (no discordance, i.e. no statistically significant deviations between experimental branches) and 1 (complete discordance).

x is the return value of a ampliconduo call.

Value

Data frame with three columns. The first column contains the sample/amplicon pair names. Second and third column harbor the corresponding Δ and Δ' values, respectively.

Author(s)

Anja Lange & Daniel Hoffmann

Examples

## load example ampliconduo data frame
data(amplicons)

## calculate the discordance between amplicon data sets of an ampliconduo data frame
dd.a <- discordance.delta(amplicons)
dd.b <- discordance.delta(amplicons, theta = 0.1)
dd.c <- discordance.delta(amplicons, printToTex = TRUE)

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/discordance.delta.Rd_%03d_medium.png", width=480, height=480)
> ### Name: discordance.delta
> ### Title: Measure Of Discordance Between Two Amplicon Data Sets
> ### Aliases: discordance.delta
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## load example ampliconduo data frame
> data(amplicons)
> 
> ## calculate the discordance between amplicon data sets of an ampliconduo data frame
> dd.a <- discordance.delta(amplicons)
> dd.b <- discordance.delta(amplicons, theta = 0.1)
> dd.c <- discordance.delta(amplicons, printToTex = TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>