kda2cytoscape.identify: Match identities with respect to given variable name

In Mergeomics: Integrative network analysis of omics data

Description

kda2cytoscape.identify searches the given data list dat within the labels according to the specified attribute (variable name). It returns the matched rows. Hence, it finds identifier numbers for the searched data list dat.

Usage

kda2cytoscape.identify(dat, varname, labels)

Arguments

dat	node ID list whose symbols or names will be collected from network node name (or symbol) list.
varname	specifies that dat will be searched among labels according to which variable (attribute). Here, gene symbols whose IDs are given, will be searched in the causal network node list according to the NODE attribute.
labels	the data list possibly including names or symbols corresponding to the given IDs in the dat data list.

Value

res	the matching rows of labels with the identifiers of given data list dat

Author(s)

Zeyneb Kurt

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

kda2cytoscape

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 <- kda2cytoscape.identify(aa, "MODULE", c("Mod1"))
bb
cc <- kda2cytoscape.identify(aa, "MODULE", c("Mod1", "Mod3"))
cc
dd <- kda2cytoscape.identify(aa, "NODE", c("GeneA"))
dd

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