compute_spill: Calculate a Spillover Matrix from Diva Controls
In rogerswt/wadeTools: Wade's Hodgepodge of Flow Cytometry Functions
View source: R/comp_compute_spill.R
compute_spill R Documentation
Calculate a Spillover Matrix from Diva Controls
Description
Calculate a spillover matrix, given compensation control FCS
files in DIVA convention.
Usage
compute_spill(ff, fsc.thresh = 30000, path = NULL, show = FALSE)
Arguments
ff
A flowFrame, used to specify fluorescence parameter names. Please note,
the parameters in ff MUST be original - that is, there must not have been a
"nice.names" or "swap.names" maneuver prior to calling this function!
fsc.thresh
A threshold to be applied on the FSC-A parameter, to
eliminate debris
path
The directory containing the comp control tubes. If not given,
path is assumed to be the current working directory.
show
Logical, should we show our work?
Details
This function computes a spillover matrix using the data in a collection
of compensation control FCS files. These files MUST reside in the same directory.
We assume that the acquisition program was Diva. Other vendors/conventions are
not currently supported.
There is an (optional) pre-gating step on FSC-A, designed to eliminate debris. The
default value for this parameter assumes no adjustment (normalization) of the
original values.
The method involves doing linear regression on the spill data, to derive the
slope of the data of y versus x, where x is the stained parameter, and y is all
other parameters. Regression occurs iteratively, eliminating outliers in an
attempt to find a robust slope.
Please note that setting show = TRUE will be very slow, and with large numbers
of parameters may overwhelm your graphics capability.
Value
The calculated spillover matrix.
rogerswt/wadeTools documentation built on Feb. 16, 2023, 7:47 a.m.
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View source: R/comp_compute_spill.R
| compute_spill | R Documentation |
Calculate a Spillover Matrix from Diva Controls
Description
Calculate a spillover matrix, given compensation control FCS files in DIVA convention.
Usage
compute_spill(ff, fsc.thresh = 30000, path = NULL, show = FALSE)
Arguments
ff |
A flowFrame, used to specify fluorescence parameter names. Please note, the parameters in ff MUST be original - that is, there must not have been a "nice.names" or "swap.names" maneuver prior to calling this function! |
fsc.thresh |
A threshold to be applied on the FSC-A parameter, to eliminate debris |
path |
The directory containing the comp control tubes. If not given, path is assumed to be the current working directory. |
show |
Logical, should we show our work? |
Details
This function computes a spillover matrix using the data in a collection of compensation control FCS files. These files MUST reside in the same directory. We assume that the acquisition program was Diva. Other vendors/conventions are not currently supported.
There is an (optional) pre-gating step on FSC-A, designed to eliminate debris. The default value for this parameter assumes no adjustment (normalization) of the original values.
The method involves doing linear regression on the spill data, to derive the slope of the data of y versus x, where x is the stained parameter, and y is all other parameters. Regression occurs iteratively, eliminating outliers in an attempt to find a robust slope.
Please note that setting show = TRUE will be very slow, and with large numbers
of parameters may overwhelm your graphics capability.
Value
The calculated spillover matrix.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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