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giannimonaco / flowAI

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flow_auto_qc() returns flowFrame named "V1" #6

Closed BexMillard closed 2 years ago

BexMillard commented 2 years ago

Hi, thanks for your time developing the flowAI package.

I noticed that when applying the flow_auto_qc() function to a flowFrame the output flowFrame no longer has its original sample name/identifier which is instead replaced by "V1". This does not seem to be an issue for flowSets.

identifier(ff) # flowFrame loaded with read.FCS() [1] "Batch0_s01.fcs" identifier(ff_qc) # flow_auto_qc() output [1] "V1"

To prevent flow_auto_qc() flowFrame outputs from being accidentally overwritten would it be possible to assign the original sample names/identifiers back to the flow_auto_qc() flowFrame output as is done for flowSets?

This would also be useful for distinguishing flowFrame QC results in the summary.txt output as all applications of the flow_auto_qc() function to individual flowFrames will currently be listed under the same filename "V1".

giannimonaco commented 2 years ago

Hi! Thank you for the suggestion! You are right that flowAI was not keeping the original names from flowFrame objects. I just fixed it now.

On Dec 6, 2021, at 4:10 PM, Rebecca Millard @.***> wrote:

Hi, thanks for your time developing the flowAI package.

I noticed that when applying the flow_auto_qc() function to a flowFrame the output flowFrame no longer has its original sample name/identifier which is instead replaced by "V1". This does not seem to be an issue for flowSets.

identifier(ff) # flowFrame loaded with read.FCS() [1] "Batch0_s01.fcs" identifier(ff_qc) # flow_auto_qc() output [1] "V1"

To prevent flow_auto_qc() flowFrame outputs from being accidentally overwritten would it be possible to assign the original sample names/identifiers back to the flow_auto_qc() flowFrame output as is done for flowSets?

This would also be useful for distinguishing flowFrame QC results in the summary.txt output as all applications of the flow_auto_qc() function to individual flowFrames will currently be listed under the same filename "V1".

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BexMillard commented 2 years ago

Thanks for the fix @giannimonaco!