cytof_cluster does not contain Rphenograph_k argument

[classycammy]

Hi, I believe that the function of "cytof_cluster" does not contain Rphenograph_k. When I run in R, I received this error:

Cluster_PhenoGraph <- cytof_cluster(xdata= combined_data_transformed_40K, method="Rphenograph", Rphenograph_k=45) Error in cytof_cluster(xdata = combined_data_transformed_40K, method = "Rphenograph", : unused argument (Rphenograph_k = 45)

Could you please advise? Thank you.

[SamGG]

Hi, Here is a dummy code that shows no problem with the latest version of cytofkit. Could you report the version you are running?

packageVersion("cytofkit")
set.seed(0); cytof_cluster(xdata = matrix(rnorm(1000), 100, 10), method = "Rphenograph", Rphenograph_k = 20)

[classycammy]

Hi, Thanks so much for the prompt reply. I truly appreciate it. I am using version 1.8.4

packageVersion("cytofkit") [1] ‘1.8.4’

When I run the function under version 1.8.4, I got this (see below for the first few lines):

cytof_cluster function (ydata = NULL, xdata = NULL, method = c("Rphenograph", "ClusterX", "DensVM", "FlowSOM", "NULL"), FlowSOM_k = 40) { method = match.arg(method)

I do appreciate any advises. Thanks very much.

[SamGG]

Quite old in fact. You found the problem: the parameter is not available in this version whereas the documentation reflects the use of the latest version. I think you should upgrade R to 3.5.0 and bioconductor 3.7. If you don't want to change your install, you could try to install cytofkit using devtools and github, but the success of such an install relies on the fact that cytofkit are resolved or could be resolved in the current R environment. Try it!

[classycammy]

Right. Thank you so much, Sam. Appreciate it tons. It is good to know that it is due to the version. I will upgrade to the version you have recommended.

[SamGG]

If this issue is solved, could you close it? Best.