summarizeFile: Compute aggregate statistics on a collection of opp or fcs...

In armbrustlab/flowPhyto: Methods for Continuous Flow Cytometry

Description

perform aggregate statistics on a particular combination of filtered opp or fcs files for a particular population.

Usage

summarizeFile(opp.paths, pop.names, output.path=getCruisePath(opp.paths[1]))

Arguments

opp.paths	Path to the raw event file to be filtered.
pop.names	Abreviated name of the population subset to be summarized.
output.path	Path to the directory where you wish to output data.

Value

a single row dataframe (with header) file of per population aggregate statistics on both channels and log meta information

Examples

example.cruise.name <- 'seaflow_cruise'
temp.out.dir <- '.'

seaflow.path <- system.file("extdata", example.cruise.name, package="flowPhyto")
file.copy(from=seaflow.path, to=temp.out.dir, recursive=TRUE)

opp.paths <- sapply(c(1,2,3), function(i) 
	system.file("extdata","seaflow_cruise","2011_001", paste(i,'.evt.opp',sep=''), 
			package="flowPhyto"))


summarizeFile(opp.paths, pop.names='nano', output.path='.')

## optionally create a resample list 
## to concatenate files conditionally on population concentrations
#resamp.list <- createResampleList(cruise.path, 
#			resample.min=500, resamp.concat.max=5)
unlink(example.cruise.name, recursive=TRUE)

armbrustlab/flowPhyto documentation built on May 10, 2019, 1:40 p.m.