gate_quad_sequential as parent gate for downstream gating in opencyto CSV template
0
0
Entering edit mode
Noël • 0
@f7429073
Last seen 2.0 years ago
Netherlands

Hi all,

I'm new to this forum so please forgive me if I'm not posting this question in the right place. I have recently started working with Opencyto package for automated data analysis of FACS data in R. I'm really enthousiastic about the package, but I'm running into an issue that i cannot seem to fix. It regards the usage of a CSV template to define the gating strategy. In this CSV file, I'm able to create relatively simple gates, but when i try to make a gate with the gate_quad_sequential gating method, things get a bit tricky. When i define the following in the CSV:

alias: A,B,C,D pop: * parent: parent dims: markerA,markerB gating_method: gate_quad_sequential gating_args: gFunc = 'mindensity'

i get the following error: Error in pops[[2]] : subscript out of bounds

when i define the following:

alias: A,B,C,D pop: +/-+/- parent: parent dims: markerA,markerB gating_method: gate_quad_sequential gating_args: gFunc = 'mindensity'

it works, but the alias of the population is overwritten by * and no further gating can be done on any of the quad gates as i cannot use them as parent in the CSV template due to the overwriting if the alias.

So basically what i want is to make a quadgate with the gate_quad_sequential method (and not the regular mindensity function in two dimensions) and i also want to be able to create subgates with these quadgates as parents within the CSV file.

Any help is greatly appreciated!

Thanks!

opencyto FlowCytometry • 630 views
ADD COMMENT

Login before adding your answer.

Traffic: 671 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