asinnorm: Computes the arcsinh ratio of a matrix in relation to the...

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

Description

Computes the arcsinh ratio of a matrix in relation to the specified column

Usage

asinnorm(mat, col, cofactor)

Arguments

mat	- The result of a call to the parsestats function
col	- The index of column to compute ratios against
cofactor	- The cofactor for arcsinh transformation; typically set as 5 for CyTOF

Value

Returns a matrix with values as the arcsinh ratio of mat normalized to selected column with the desired cofactor

Examples

#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)

athrom/CytobankAPIstats documentation built on May 14, 2019, 5:24 p.m.