ssea.start.identify: Convert identities to indices for MSEA

In Mergeomics: Integrative network analysis of omics data

Description

ssea.start.identify finds matching identities for the given variable name. It searches the members of dat among the members of labels with respect to the varname attribute, returns the matching rows of the dat.

Usage

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

Arguments

dat	data list (source) of the identities that will be searched. e.g. the information after merging of overlapped genes (containing shared markers)
varname	search and match will be performed with respect to which attribute (MODULE or NODE or MARKER)
labels	the place, where the identities of dat will be searched and matched.

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

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

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