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\name{ssea.start.identify}
\alias{ssea.start.identify}
\title{
Convert identities to indices for MSEA
}
\description{
\code{\link{ssea.start.identify}} finds matching identities for the given
variable name. It searches the members of \code{dat} among the members of
\code{labels} with respect to the \code{varname} attribute, returns the
matching rows of the \code{dat}.
}
\usage{
ssea.start.identify(dat, varname, labels)
}
\arguments{
\item{dat}{data list (source) of the identities that will be searched.
e.g. the information after merging of overlapped genes (containing shared
markers) }
\item{varname}{search and match will be performed with respect to
which attribute (MODULE or NODE or MARKER) }
\item{labels}{the place, where the identities of \code{dat} will be
searched and matched. }
}
\value{
\item{res}{matched rows of \code{dat} among the members of \code{labels}
list according to the \code{varname} attribute}
}
\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
}
\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.
}
\author{
Ville-Petteri Makinen
}
\seealso{
\code{\link{ssea.start}}
}
|
