Question: flowCore: 'truncate_max_range' argument in 'read.flowSet'
0
2.6 years ago by
Zurich, Switzerland
Lukas Weber0 wrote:

Hi,

I have a question about reading in data from multiple FCS files with read.flowSet from the flowCore package.

By default, both read.FCS and read.flowSet truncate values outside the specified instrument measurement range. The read.FCS function (for a single FCS file) also includes an argument to disable this, truncate_max_range = FALSE, which I have found useful in case the measurement range hasn't been specified correctly. This was also discussed previously on this list, e.g. this question: readFCS truncates the data that is out of instrument range

However, there doesn't seem to be a similar argument in read.flowSet (for reading in multiple files). Is there any way to disable truncation of values with read.flowSet? I could simply use lapply and read.FCS, but it would be useful to have this option available directly within read.flowSet.

Best regards,

Lukas

flowcore • 469 views
modified 2.6 years ago • written 2.6 years ago by Lukas Weber0
1
2.6 years ago by
Jiang, Mike1.2k
Jiang, Mike1.2k wrote:

I've pushed the fix to flowCore 1.40.5. or you can devtool::install_github("RGLab/flowCore", ref = "trunk") if you can't wait until BioC build the release.

Alternatively, you can use 'read.ncdfFlowSet which already supports this feature and is generally favored than 'read.flowSet' due to its scalability.

0
2.6 years ago by
Zurich, Switzerland
Lukas Weber0 wrote:

Great, thanks for the quick reply and update. I'll also look into using read.ncdfFlowSet` in future.

Lukas