concordance {gespeR} | R Documentation |
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.
concordance(..., min.overlap = 10, cor.method = "spearman", rbo.p = 0.98, rbo.k = NULL, rbo.mid = 0, uneven.lengths = TRUE)
... |
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 |
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 |
Fabian Schmich
data(stabilityfits) conc <- concordance(gsp(stabilityfits$A), gsp(stabilityfits$B), gsp(stabilityfits$C), gsp(stabilityfits$D)) plot(conc)