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giannimonaco / flowAI

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Update flow_auto_qc to use flowCore::identifier. Set default FileType… #2

Closed DillonHammill closed 4 years ago

DillonHammill commented 4 years ago

@giannimonaco, just some fixes to address https://github.com/DillonHammill/CytoExploreR/issues/59. Some FCS files do not contain $FIL slot so it is better to use flowCore::identifier() which first checks for $GUID then $FIL then $FILENAME. The other issue involves the FileType argument which is only set when fcsfiles contains the names of the files. This is fine, except when I flowSet is supplied and timestep is missing. To fix this I updated the code to set the FileType as "FCS" when a flowFrame or flowSet is supplied. There some warnings generated with the newer flowCore that involve depreciated description<- calls you may want to track them down and switch to using keyword instead. Looks like I am using a new version of Roxygen so the format of the docs has changed slightly.

giannimonaco commented 4 years ago

@DillonHammill thank you for this! I accepted the merging request and will check the description<- calls too.

giannimonaco commented 4 years ago

Just changed all the description<- calls with the keyword function. Thank you for suggesting this!