| Title: | flowBeads: Analysis of flow bead data |
|---|---|
| Description: | This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation. |
| Authors: | Nikolas Pontikos |
| Maintainer: | Nikolas Pontikos <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.43.0 |
| Built: | 2024-07-03 05:32:40 UTC |
| Source: | https://github.com/bioc/flowBeads |
Bioconductor package for working with calibration beads in flow cytometry. Based on flowCore package.
Nikolas Pontikos [email protected]
Absolute normalise to align peaks of bead.data to MEF.
bead.data |
|
mef.data |
A list of affine functions from transformed MFI relative coordinates to transformed MEF absolute coordinates.
Extension of flowFrame specific for bead
data.
The constructor take as arguments the FCS file and the file containing the MEF values of the beads on the different detector channels
BeadFlowFrame(fcs.filename, bead.filename)BeadFlowFrame(fcs.filename, bead.filename)
fcs.filename |
The file name of the FCS to load.
File is loaded with the
|
bead.filename |
The file name of the MEF configuration files indicating the type of beads in the FCS file. The bead.file is read with read.csv. |
fcs.filename:The file name of the FCS file from which to read.
bead.filename:The file name of the bead config file.
beads.mef:The
data.frame containing the MEF of the bead
populations on different channels.
trans:The transform to linearise
the fluorescence.
inv.trans:The inverse
transform of .
gateBeads gates on all channels, apply scatter
gate first. Find parameters in MEF data.frame which are
also present in BeadFlowFrame The number of expected bead
populations is by default six and it is assumed that that
there is the same number of beads in each population.
bead.data |
The BeadFlowFrame object to gate. |
K |
The number of bead populations expected. |
verbose |
Whether to print debug information. |
data(beads1) gateBeads(beads1)data(beads1) gateBeads(beads1)
GatedBeadFlowFrame
labels |
The resulting labels of the clustering assigning each event to a different bead population. |
clustering.stats |
Three dimensional array summarising the stats per channel and population. |
mef.tranform |
The list of MEF transforms |
Generate an HTML report from a Markdown template using knitr.
bead.data |
|
output.file |
name of the file to which to output the HTML report. |
knitr
Returns transform function. The default is the logicle transform for FCS 3 and the log10 transform for FCS 2.
Input parameters are to be provided in decades
mefTransform(transformationId = "mefTransform", alpha, beta)mefTransform(transformationId = "mefTransform", alpha, beta)
transformationId |
The name of the transformation. |
alpha |
The intercept of the MEF transform. |
beta |
The slope of the MEF transform. |
Plot the results of the clustering. Plot only the requested channel which should have a corresponding entry in the MEF files
Ungated bead data, simply draw all channels individually (no colours).
If no argument specified then plot all parameters
Relative normalise to align peaks of bead.data1 to those of bead.data2 Returns a list of affine functions from transformed MFI day one coordinates to transformed MFI day two coordinates. This permits comparison of channels across two days, provided the detector is stable, even in the absence of absolute MEF values.
bead.data1: |
|
bead.data2: |
|
A list of affine functions from MFI day one coordinates to MFI day two coordinates.
Given bead.data and a flow.data apply the MEF transform
to matching channels in flow.data.
bead.data |
The GatedBeadFlowFrame object containing the MEF transform. |
flow.data |
The flowFrame object on which to apply the transform. |