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Last data update: 2014.03.03

R: Evaluate the concordance between Phenotype objects

concordance

R Documentation

Evaluate the concordance between Phenotype objects

Description

Measures include the correlation (rho) between pairs of phenotypes for the same gene, the rank biased overlap (rbo) of the top and bottom of ranked lists, and the Jaccard index (J) of selected genes.

Usage

concordance(..., min.overlap = 10, cor.method = "spearman", rbo.p = 0.98,
  rbo.k = NULL, rbo.mid = 0, uneven.lengths = TRUE)

Arguments

`...`	The phenotypes to be evaluated for concordance
`min.overlap`	The minimum number of overlapping genes required
`cor.method`	A character string indicating which correlation coefficient is to be computed
`rbo.p`	The weighting parameter for rank biased overlap (rbo) in [0, 1]. High p implies strong emphasis on top ranked elements
`rbo.k`	The evaluation depth for rank biased overlap extrapolation
`rbo.mid`	The mid point to split a ranked list, e.g. in order to split positive and negative scores choose mid=0
`uneven.lengths`	Indicator if lists have uneven lengths

Value

A concordance object with the following elements:

`pair.test`	Indicator of compared phenotypes
`cor`	The correlation between pairs of phenotypes for the same gene
`rbo.top`	The rank biased overlap of genes evaluated at the top of the ranked list
`rbo.bottom`	The rank biased overlap of genes evaluated at the bottom of the ranked list
`jaccard`	The Jaccard index of selected genes

Author(s)

Fabian Schmich

Examples

data(stabilityfits)
conc <- concordance(gsp(stabilityfits$A), gsp(stabilityfits$B),
gsp(stabilityfits$C), gsp(stabilityfits$D))
plot(conc)

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)

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> library(gespeR)
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/gespeR/concordance.Rd_%03d_medium.png", width=480, height=480)
> ### Name: concordance
> ### Title: Evaluate the concordance between Phenotype objects
> ### Aliases: concordance
> 
> ### ** Examples
> 
> data(stabilityfits)
> conc <- concordance(gsp(stabilityfits$A), gsp(stabilityfits$B),
+ gsp(stabilityfits$C), gsp(stabilityfits$D))
> plot(conc)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>