cytofAsinh() function not available

[agataraczynska]

Hello,

I would like to use cytofAsinh() function to transform my data, but I do not have this function in my cytofkit package. I had problems installing cytofkit package. In the end I somehow installed ‘cytofkit’ version 1.12.0 manually by downloading zip from Bioconductor and placing it in appropriate directory on my computer.

Is the function cytofAsinh() only available through the bulky cytofkit() function?

[SamGG]

Hi,
If you simply need the cytofAsinh function (which should be applied to CyTOF data) you could simply copy the code starting at

cytofkit/R/cytof_preProcess.R

Lines 241 to 258 in c4f93e5

	#' Noise reduced arsinh transformation
	#'
	#' Inverse hyperbolic sine transformation (arsinh) with a cofactor of 5, reduce noise from negative values
	#' Adopted from Plos Comp reviewer
	#'
	#' @param value A vector of numeric values.
	#' @param cofactor Cofactor for asinh transformation, default 5 for mass cytometry data.
	#' @noRd
	#' @return transformed value
	cytofAsinh <- function(value, cofactor = 5) {
	value <- value-1
	loID <- which(value < 0)
	if(length(loID) > 0)
	value[loID] <- rnorm(length(loID), mean = 0, sd = 0.01)
	value <- value / cofactor
	value <- asinh(value) # value <- log(value + sqrt(value^2 + 1))
	return(value)
	}

Best.

[agataraczynska]

Thank you very much! It worked for me.