Question: flowCore: 'truncate_max_range' argument in 'read.flowSet'
0
gravatar for Lukas Weber
2.8 years ago by
Johns Hopkins University
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 • 483 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Lukas Weber0
Answer: flowCore: 'truncate_max_range' argument in 'read.flowSet'
1
gravatar for Jiang, Mike
2.8 years ago by
Jiang, Mike1.2k
(Private Address)
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.

ADD COMMENTlink written 2.8 years ago by Jiang, Mike1.2k
Answer: flowCore: 'truncate_max_range' argument in 'read.flowSet'
0
gravatar for Lukas Weber
2.8 years ago by
Johns Hopkins University
Lukas Weber0 wrote:

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

Lukas

ADD COMMENTlink written 2.8 years ago by Lukas Weber0
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