```
#' Collapse a sample's MALDIquant peak objects into a single peak object
#'
#' @param sampleIDs sampleIDs
#' @param peakList peakList
#'
#' @export
#' @return a single trimmed and binned MALDIquant peak object
smallMolDFtoNetwork <- function(peakList,
sampleIDs){
smallNetwork <- MALDIquant::intensityMatrix(peakList)
temp <- NULL
rownames(smallNetwork) <- sampleIDs
smallNetwork[is.na(smallNetwork)] <- 0
smallNetwork <- ifelse(smallNetwork > 0,1,0)
smallNetwork <- as.data.frame(smallNetwork)
#The network is weighted by the inverse of percentage of presence of the peak, this de-emphasizes commonly occuring peaks and "pulls" rarer peaks closer to their associated sample
smallNetwork[ , colnames(smallNetwork)] <- sapply(smallNetwork[ , colnames(smallNetwork)],
function(x) ifelse(x == 1, 1 / sum(x), x))
#Create a matrix readable by Gephi as an edges file
smallNetwork <- cbind(rownames(smallNetwork),smallNetwork)
smallNetwork <- reshape2::melt(smallNetwork)
# Remove zero length edges
smallNetwork <- base::subset(smallNetwork, smallNetwork$value != 0)
colnames(smallNetwork) <- c("Source","Target","Weight")
# Round m/z values to two decimals, use sprintf to preserve trailing zeros
smallNetwork$Target <- sprintf(as.numeric(as.matrix(smallNetwork$Target)), fmt = '%#.2f')
smallNetwork$Source <- as.character(smallNetwork$Source)
smallNetwork$Target <- as.numeric(smallNetwork$Target)
smallNetwork$Weight <- as.numeric(smallNetwork$Weight)
return(smallNetwork)
}
```

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