Nothing
runLIAYSON <- function(X, S, sName, mingps = 20, GRCh = 37, h = 0.2, minSegLength = 1e+06, outD = NULL) {
message(paste("Running LIAYSON on", sName, "..."))
## Genes expressed per cell:
gpc = apply(X > 0, 2, sum)
names(gpc) = colnames(X)
## Expression per segment per cell:
cps <- matrix(NA, nrow(S), ncol(X))
rownames(cps) = rownames(S)
colnames(cps) = colnames(X)
eps <- gps <- cps
tmp = aggregateSegmentExpression(X, S, GRCh = GRCh, mingps = 1)
if(is.null(tmp)){
print("BiomaRt Web service for annotation of gene locations is not available. Aborting.")
return()
}
eps[rownames(tmp$eps), ] = tmp$eps
gps[rownames(tmp$gps), ] = tmp$gps
## Copy number per segment per cell:
iK = rownames(tmp$gps)[apply(tmp$gps, 1, median) >= mingps]
cps[iK, ] = segmentExpression2CopyNumber(tmp$eps[iK, ], gpc, cn = S[iK, "CN_Estimate"], seed = 0, nCores = ceil(length(iK)/2), stdOUT = paste0("log.", sName))
## Cluster cells
cps = cps[apply(!is.na(cps), 1, any), ]
outc = clusterCells(cps, h = h, minSegLength = minSegLength)
## Save output
if (!is.null(outD)) {
saveClusteredCells(outc, expression = X, ccMembership = list(G1Malignant = names(outc$sps)), sName = sName, outD = outD)
}
return(outc)
}
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