Entering edit mode
I am attempting to make some simple gates on single colored controls. I first read in all the .fcs files of interest using read.FCS
frames <- lapply(dir(fcs_path, full.names = TRUE), read.FCS, truncate_max_range = FALSE)
I know that the third frame in this list is the single colored control for CD3, so I pull that frame from the list:
CD3_frame <- frames[[3]]
This gives me a single flowFrame:
class(CD3_frame)
[1] "flowFrame"
attr(,"package")
[1] "flowCore"
Now when I attempt to use flowDensity in its most basic form, I get this error.
CD3_frame.gate <- flowDensity(CD3_frame, channels = c("FL4-A", "FSC-A"),
positions = c(T, NA))
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘flowDensity’ for signature ‘"flowFrame", "character", "missing", "missing"’
I have successfully used flowDensity in the past using this same flow and have not run into this problem. Is there something obvious that I am missing here?