make.cytoFrame: Turns a flowFrame into a cytoFrame

In yannabraham/cytoCore: extending flowCore for CyTOF data analysis

Description

After loading CyTOF data as FCS, updates the parameters slot of the flowFrame so that isotopes & channel name are clearly separated; adds a type column to explicitly set parameter type

Usage

make.cytoFrame(ff, channels)

Arguments

ff	a flowFrame object
channels	a list of channels sorted by type (see details)

Details

Channels

Value

a flowFrame object with extra type and isotope columns

Author(s)

Yann Abraham

Examples

ff <- read.FCS(system.file("extdata","Staurosporine_cd4+_H05.fcs",package="cytoCore"))

channels <- list(CyTOF=c('Time','Cell_length'),
     DNA=c('DNA-1','DNA-2'),
     phenotypic=c('CD3','CD45','CD4','CD20','CD33','CD123','CD14','HLA-DR','IgM','CD7'),
     functional=c('pNFkB','pp38','pStat5','pAkt','pStat1','pSHP2','pZap70','pStat3','pSlp76','pBtk','pPlcg2','pErk','pLat','pS6'),
     barcode=c('BC1','BC2','BC3','BC4','BC5','BC6','BC7')
)

cf <- make.cytoFrame(ff,channels)

yannabraham/cytoCore documentation built on May 4, 2019, 2:29 p.m.