Mergeomics (version 1.0.0)

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

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

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

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