R/asinnorm.R

In athrom/CytobankAPIstats: Computes Signaling and Population Stats for Cytometry Data on Cytobank using 'CytobankAPI'

#' Computes the arcsinh ratio of a matrix in relation to the specified column
#It takes a matrix of statistics with columns correspondings to different samples of interest (mat)
#It also takes the column of the matrix by which to normalize the data (col) and the 
#cofactor with which to compute the arcsinh ratios (cofactor). Note that the cofactor is typically 5 for CyTOF data 
#but may need to be manually adjusted.
#' @param  mat - The result of a call to the parsestats function
#' @param  col - The index of column to compute ratios against
#' @param  cofactor - The cofactor for arcsinh transformation; typically set as 5 for CyTOF
#' @return Returns a matrix with values as the arcsinh ratio  of mat normalized to selected column with the desired cofactor
#' @examples \donttest{
#' #Example starting with obtaining data from Cytobank
#' library(CytobankAPI)
#' popsofinterest<-c("CD4 T cells","NK cells")
#' cyto_session <- authenticate(site="premium", username="myusername", password="mypassword")
#' exptno<-2
#' popsinterest<-getpops(popsofinterest,exptno,cyto_session)
#' fcs<-getfcsfiles(exptno,cyto_session)
#' type=TRUE
#' results<-analyzedata(cyto_session,markersofinterest,popsofinterest,exptno,type)
#' asinnorm(results,col=2,cofactor=5)}
#' 
#' #Example with simple data matrix
#' data<-matrix(1:9,nrow=3,ncol=3,byrow=TRUE)
#' colnames(data)<-c("Control","Patient1","Patient2")
#' rownames(data)<-c("Marker1","Marker2","Marker3")
#' #Normalizing patient data to control sample with cofactor of 5
#' asinnorm(data,1,5)
#' @export
asinnorm<-function(mat,col,cofactor){
  norm<-asinh(mat[,col]/cofactor)
  tmat<-asinh(mat/cofactor)
  x<-tmat-norm
  return(x)
}