cytofCore.extract.R: Extraction of cells from CyToF IMD files

Description Usage Arguments Details Value Author(s) References

View source: R/extract.R

Description

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

Usage

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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)

Arguments

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.

Details

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.

Value

cells.found

Matrix of cells

quality

Quality metric, in [0,1] where 0 is lowest quality and 1 is highest quality

Author(s)

Michael Linderman (mlinderm@stanford.edu)

References

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


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