How to write a flowFrame from a matrix
2
0
Entering edit mode
@allenby-mark-6637
Last seen 7.3 years ago
All, flowFrames can be created by .FCS files using read.FCS, I was wondering if I could create a flowFrame from a matrix, The matrix will be in the identical form of the exprs() output for a flowFrame, so that I could extract data to a raw matrix, custom-manipulate, then remake the flowFrame and use flowCore functions again. I am sure I am overlooking some simple function here, any help? Best reguards, Mark Allenby PhD, Imperial College London
flowCore flowCore • 2.5k views
ADD COMMENT
0
Entering edit mode
@kipper-fletez-brant-6421
Last seen 3.7 years ago
United States
Hi Mark, I'm not sure if you've seen the flowCore reference guide [1] but it explains how to create a flowFrame. In addition to your matrix of observations, you also need to fill the slots for 'parameters' and 'description'; this can done using either the 'new()' command or a built-in flowFrame constructor. [1] http://www.bioconductor.org/packages/release/bioc/manuals/flowCore/man /flowCore.pdf, see pg 51 On Tue 08 Jul 2014 01:44:57 PM EDT, Allenby, Mark wrote: > All, > > flowFrames can be created by .FCS files using read.FCS, I was wondering if I could create a flowFrame from a matrix, The matrix will be in the identical form of the exprs() output for a flowFrame, so that I could extract data to a raw matrix, custom-manipulate, then remake the flowFrame and use flowCore functions again. > > I am sure I am overlooking some simple function here, any help? > > Best reguards, > > Mark Allenby > PhD, Imperial College London > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENT
0
Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
(Private Address)
|openCyto| package has an internal function for loading matrix(first row must contains the channel or marker name) from csv. e.g. |> fr <- openCyto:::.read.FCS.csv("local_output/test.csv") > fr flowFrame object'anonymous' with2 cells and2 observables: name desc range minRange maxRange FSC-A FSC-ANA 11 1 11 SSC-A SSC-ANA 12 2 12 1 keywords are storedin the'description' slot | On 07/09/2014 03:00 AM, bioconductor-request@r-project.org wrote: > Subject: > [BioC] How to write a flowFrame from a matrix > From: > "Allenby, Mark" <mark.allenby@imperial.ac.uk> > Date: > 07/08/2014 10:44 AM > > To: > "bioconductor@r-project.org" <bioconductor@r-project.org> > > > All, > > flowFrames can be created by .FCS files using read.FCS, I was wondering if I could create a flowFrame from a matrix, The matrix will be in the identical form of the exprs() output for a flowFrame, so that I could extract data to a raw matrix, custom-manipulate, then remake the flowFrame and use flowCore functions again. > > I am sure I am overlooking some simple function here, any help? > > Best reguards, > > Mark Allenby > PhD, Imperial College London > > [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 210 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6