Description Details Author(s) See Also Examples
Simplifies the usage of flowCore with CyTOF data by providing simple function to load, annotate and deconvolute barcodes for CyTOF experiments
Package: | cytoCore |
Type: | Package |
Version: | 0.1 |
Date: | 2013-11-13 |
License: | CC BY-NC-SA |
Yann Abraham Maintainer: Yann Abraham <yann.abraham@novartis.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | # load example data
ff <- read.FCS(system.file("extdata","Staurosporine_cd4+_H05.fcs",package="cytoCore"))
# specify channels
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')
)
# annotate flowFrame
cf <- make.cytoFrame(ff,channels)
# normalize channels
cf <- do.transform(cf,type=c('phenotypic','functional'))
# deconvolute barcodes
bc.cf <- do.deconvolution(cf,diagnostics=FALSE,add=FALSE)
table(droplevels(bc.cf$barcode)) # some noise in the deconvolution
# split the flowFrame using the barcode
cSet <- split(cf,bc.cf$barcode,flowSet=TRUE)
# correct the range for individual files
cSet <- fsApply(cSet,correct.range)
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