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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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Improvement Request: downsample to the maximum of either the file event count or target #89

Open tjchen opened 10 years ago

tjchen commented 10 years ago

in downsample.R please give the option of downsampling to the maximum of either the file event count or target. Currently it is a hard threshold on the event count and fails if the number of events in the file are less than the downsampling event number.

esimonds commented 10 years ago

Good idea. While we're mucking around I there, is support for "percent" of cell events currently supported in Driver.R? (note that I'm not talking about "percentile of density"). It's the default on Cytobank SPADE but I suspect it was an improvement on their end.

On Saturday, March 1, 2014, TJ Chen notifications@github.com wrote:

in downsample.R please give the option of downsampling to the maximum of either the file event count or target. Currently it is a hard threshold on the event count and fails if the number of events in the file are less than the downsampling event number.

Reply to this email directly or view it on GitHubhttps://github.com/nolanlab/spade/issues/89 .

zbjornson commented 10 years ago

@esimonds yep, it's there:

(... in driver.r...)
downsampling_target_number=NULL,
downsampling_target_pctile=NULL,
downsampling_target_percent=0.1,
(...)