gespeR (version 1.4.2)

concordance: 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

See Also

Phenotypes

plot.concordance

rbo

Examples

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