aggregateNeighbors produces NA

BodenmillerGroup / imcRtools

An R package for handling and analysing imaging mass cytometry data

https://bodenmillergroup.github.io/imcRtools/

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aggregateNeighbors produces NA #101

Closed roskcl closed 1 year ago

roskcl commented 1 year ago

Hello, I am running the Cellular neighborhood analysis from the steinbock pipeline. However, when I aggregateNeighbors by expression NAs are produced for some cells like in the image below. This stops kmeans clustering from working for neighbourhood detection. Do you have any suggestion on what could be done to overcome this issue? Would substituting the NAs for 0s be acceptable? Thank you very much for your help!

nilseling commented 1 year ago

Hi @roskcl

yes, those cells don't have any neighboring cells. You can replace the NAs with 0 to perform the clustering.