cytofCore.extract.R: Extraction of cells from CyToF IMD files
In nolanlab/cytofCore: cytofCore: Analysis tools for CyToF Mass Cytometer Data

Description Usage Arguments Details Value Author(s) References

View source: R/extract.R

Identifies and extracts cells from CyToF IMD files using simple thresholding algorithm. Two implementations are availabe: in pure R, and with a C++ core.

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cytofCore.extract.R(imd, conf, pulse_thresh = 3, num_pushes = NULL, thresh = 10, sigma = 3, num_sigma = 3, min_length = 10, max_length = 75, noise.subtraction = TRUE, noise.min.length = 30, slope.filter = TRUE, freq = 77000)
cytofCore.extract.native(imd, conf, pulse_thresh = 3, num_pushes = .Machine$integer.max, thresh = 10, sigma = 3, num_sigma = 3, min_length = 10, max_length = 75, noise.subtraction = TRUE, noise.min.length = 30, slope.filter = TRUE, freq = 77000)

`imd`	IMD file
`conf`	CyToF conf file or matrix.
`pulse_thresh`	Pulse threshold used in dual count computation.
`num_pushes`	Number of pushes to read. Default values reads to end of file.
`thresh`	Threshold for start of a cell.
`sigma`	Standard deviation of guassian filter applied to time series prior to thresholding.
`num_sigma`	Number of sigma to extend gaussian filter.
`min_length`	Minimum length of cell in pushes.
`max_length`	Maximum length of cell in pushes.
`noise.subtraction`	Subtract noise from cell counts.
`noise.min.length`	Minimum length for valid noise region in pushes.
`slope.filter`	Set cell quality to zero if slope has more than one zero crossing.
`freq`	Number of pushes per second.

Extracts cells from CyToF IMD file with conservative algorithm similar but not identical to that used by manufacturer's software. ".R" is a native R implementation, while ".native" is a C++-based implementation that is substantially more performant.