Mergeomics (version 1.0.0)

kda.start.identify: Convert identities to indices for wKDA

Description

kda.start.identify searches the members of dat among the members of labels with respect to the varname attribute, returns the matching rows of the dat.

Usage

kda.start.identify(dat, varname, labels)

Arguments

dat

data list of the identities that will be searched

varname

search will be performed with respect to which attribute (MODULE or NODE)

labels

the place, where data list (i.e. dat) will be searched

Value

res

matched rows of dat among the members of labels list according to the varname attribute

References

Shu L, Zhao Y, Kurt Z, Byars S, Tukiainen T, Kettunen J, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. bioRxiv doi: http://dx.doi.org/10.1101/036012

See Also

kda.analyze, kda.finish, kda.prepare, kda.start

Examples

## Converts identities (either module names or gene names) to the indices
aa<- data.frame(MODULE=c("Mod1", "Mod1", "Mod2", "Mod2", "Mod3"), 
NODE=c("GeneA", "GeneC", "GeneB", "GeneC", "GeneA"))
aa
bb <- kda.start.identify(aa, "MODULE", c("Mod1"))
bb
cc <- kda.start.identify(aa, "MODULE", c("Mod1", "Mod3"))
cc
dd <- kda.start.identify(aa, "NODE", c("GeneA"))
dd