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Create CYT object in CytoTree in R

I want to create a CytoTree CYT object in R to analyse my .FCS files. When I am using the Quick start code in the package description, I will always get an error when running the createCYT() function that says:

Error in createCYT(raw.data = fcs.data, normalization.method = "log") : 2022-09-26 15:46:26 meta.data must be a data.frame

As the function should not rely on any meta data and that object is optional, I do not know how to solve the error.

Here is the description:

https://ytdai.github.io/CytoTree/quick-start.html#quick-start-code

I thank you very much in advance for your help!

BR

Solution

  • I have encountered same problem previously. In the end it worked only when the data.frame was added (yes, even though it should not depend on it). Here is how:

    meta.data <- data.frame(cell = rownames(fcs.data), stage = gsub(".fcs.+", "", rownames(fcs.data)))

meta.data$stage <- factor(as.character(meta.data$stage))

    You may as well have a look at the Cytotree PDF in case of more issues.