do.transform: Applies transformation to selected columns

In yannabraham/cytoCore: extending flowCore for CyTOF data analysis

Description

Applies a specific transformation to all columns specified either by name or type

Usage

do.transform(ff, cols=NULL, type=NULL, fun=arcsinhTransform())

Arguments

ff	a flowFrame object
cols
type	a column type to transform
fun	the transformation function to apply (defaults to arcsinhTransform)

Details

Type can be a single character string or a vector of column types

Value

a flowFrame object with specified transformation applied to specified columns or types

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)

# apply default transformation by column name
cf <- do.transform(cf,cols=c('DNA.1','DNA.2'))
# apply default transformation by type
cf <- do.transform(cf,type=c('phenotypic','functional'))

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