readSeaflow: Read a SeaFlow File

In armbrustlab/flowPhyto: Methods for Continuous Flow Cytometry

Description

reads a binary SeaFlow event file and converts into an event dataframe

Usage

readSeaflow(file.path, column.names = EVT.HEADER, column.size = 2, 
		count.only=FALSE,  transform=TRUE, add.yearday.file=FALSE)

Arguments

file.path	System path to the binary seaflow event file.
column.names	Names of the channels. By default it uses the standard SeaFlow channels described in 'EVT.HEADER' that are [1] "time" [2] "pulse_width" [3] "D1" [4] "D2" [5] "fsc_small" [6] "fsc_perp" [7] "fsc_big" [8] "pe" [9] "chl_small" [9] "chl_big"
column.size	Sizes in bytes of the columns. Set up at 2 by default
count.only	Just read the first line of the file (the event/line count). Use to check the conversion of the binary file. FALSE by default
transform	Log-transform the data
add.yearday.file	append the year_day and file number as two final columns in the returned dataframe.

Value

returns a seaflow dataframe

Examples

opp.file.path <- system.file("extdata","seaflow_cruise","2011_001", "1.evt.opp",
				package="flowPhyto")

opp <- readSeaflow(opp.file.path)

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