do.qc: Performs standard Quality Control on a flowFrame object

In yannabraham/cytoCore: extending flowCore for CyTOF data analysis

Description

The function generates a set of quality control plots, checking basic features of the flowFrame object

Usage

do.qc(ff, cols=NULL, type=NULL, out.dir='.')

Arguments

ff	a flowFrame object
cols	a list of columns to transform
type	a column type to transform
out.dir	the directory where the image will be saved

Details

Cols and type can be a single character string or a vector of column types. CyTOF-specific columns (Leading_push, Time, Cell_length) are included by default.

Value

Images corresponding to standard quality control plots are saved to out.dir. Function returns an invisible NULL.

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')
)

# turn the flowFrame into a cytoFrame
cf <- make.cytoFrame(ff,channels)

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

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