Mergeomics (version 1.0.0)

kda2himmeli.identify: Match identities with respect to given variable name

Description

kda2himmeli.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

kda2himmeli.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 labels or names of labels with the IDs of dat list

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

kda2himmeli

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 <- kda2himmeli.identify(aa, "MODULE", c("Mod1"))
bb
cc <- kda2himmeli.identify(aa, "MODULE", c("Mod1", "Mod3"))
cc
dd <- kda2himmeli.identify(aa, "NODE", c("GeneA"))
dd