cytofCore.read.imd: Read an CyToF IMD file

In nolanlab/cytofCore: cytofCore: Analysis tools for CyToF Mass Cytometer Data

Description

Read CyToF IMD binary file and return intensity/pulse data or dual count data

Usage

cytofCore.read.imd(file, analytes = NULL, conf = NULL, pulse_thresh = 3, start_push = 0, num_pushes = NULL)

Arguments

file	IMD file
analytes	Vector of analyte names. Length of vector must match number of analytes in IMD file. If NULL, conf must be provided.
conf	CyToF conf file or matrix. If conf data is specified, only dual counts are returned.
pulse_thresh	Pulse threshold used in dual count computation
start_push	Starting push when reading from middle of file
num_pushes	Number of pushes to read. NULL reads to end of file.

Details

Reads CyToF IMD binary file.

IMD file contains intensity (I) and pulse data (P) for all analytes and pushes. Format of each push is

I_analyte0 P_analyte0 I_analyte1 ...

where all values are 16-bit unsigned integers. File starts with push 0.

Dual counts are calculated as:

dual = round(intensity * slope + intercept) if (dual < pulse_thresh) dual = max(dual, pulse)

Value

intensity	Intensity data
pulse	Pulse data
dual	Dual counts

Author(s)

Michael Linderman ([e-mail])

References

Bandura, et al. Analytical Chemistry 81:6813-6822, 2009.

nolanlab/cytofCore documentation built on May 18, 2020, 11:51 a.m.