Get error message while using openCyto:::.flowClust.2d

[hsiuhong1]

I am able to use the followings:

openCyto:::.mindensity rectangleGate openCyto:::.singletGate openCyto:::.boundary

When I tried to use openCyto:::.flowClust.2d, I got the following error message: Error in as.character.default(x) : no method for coercing this S4 class to a vector

[mikejiang]

These are internal private APIs not meant to be used directly by the end user. Try to always stick with public exported version of these functions, that is gate _*

[hsiuhong1]

Hi Mike,

I still got the same error message.

Below is the code: chn5 <- c("APC-H7-A", "SSC-A") gmonocyte <- gate_flowclust_2d(fs_Offaxis, channels = chn5, K = 1, target = c(2.5e5,5e4), quantile = 0.95)

Error message: Error in as.character.default(x) : no method for coercing this S4 class to a vector

I can provide the full script if it is needed.

Many thanks for your help.

Siu-hong

[mikejiang]

Please take a look at the documentation of this API ?openCyto::gate_flowclust_2d, it takes a flowframe and xChannel, yChannel as input

[hsiuhong1]

Hi Mike,

Thanks.

I am able to apply the gate_flowclust_2d to a flowframe. However, if I apply it to the flowset, I got the same error message.

For the flowset I used, it is originally a cytoset. I use the function cytoset_to_flowSet to convert the cytoset to flowset.

Any insight is appreciated.

Thanks.

Siu-hong

[mikejiang]

Again, these gating functions only work with a single flowframe, if you want to work with flowset, you have to write a loop through the flowset, within the loop, extract flowframe from the flowset, then you can apply the function there, Actually you don't even need to convert to flowset,Just loop through cytoset directly for example

gates=lapply(sampleNames(cs), function(sn){
    cf = cs[[sn]]
    fr = cytoframe_to_flowFrame(cf)
    gate_flowclust_2d(fr,"APC-H7-A", "SSC-A",  K = 1, target = c(2.5e5,5e4), quantile = 0.95)
    })

[hsiuhong1]

Thanks, I am able to get through it.