function to access IMscores

[dimalvovs]

currently the output of getInteractingGenes or getPairwiseInteractingGenes if a large object not necessarily needed to the end user. this stub is abut introduction an extractor that would take SpaceMarkers object as input and produce a simple imscores data frame, containing one Gene colmn, one column per interacting pair, and hold the SpaceMarkerMetric in cells.

[orian116]

@atuldeshpande had done this in one of his analysis notebooks. Here is a possible function that I wrapped the code in

getScores <- function(spaceMarkers){
ind <- which(sapply(spaceMarkers,function(i) length(i$interacting_genes))>0)
interactionMarkerScores <- lapply(
ind,function(i) spaceMarkers[[i]]$interacting_genes[[1]][,c(
"Gene","SpaceMarkersMetric")])
IMscores <- Reduce(function(x, y) merge(x, y, by="Gene"),
interactionMarkerScores)
rownames(IMscores) <- IMscores$Gene
IMscores <- IMscores[,-1]
names(IMscores) <- names(interactionMarkerScores)
return(IMscores)
}