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

In Mergeomics: Integrative network analysis of omics data

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

Author(s)

Ville-Petteri Makinen

References

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

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

Mergeomics documentation built on Nov. 8, 2020, 6:58 p.m.