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nolanlab / spade

SPADE: Spanning Tree Progression of Density Normalized Events
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SPADE.driver #127

Closed gdreiman1 closed 7 years ago

gdreiman1 commented 7 years ago

I'm following the code listed in the Nature Methods Paper, as I am trying to learn how to use Spade for analyzing non-cytometry data. However, when I try to run SPADE.driver I get the following error message: SPADE.driver(files='input_dir', out_dir='output_dir', transforms='transforms') Error in if (length(files) == 1 && file.info(files)$isdir) { : missing value where TRUE/FALSE needed

Can somebody help me understand this? I am relatively new to R.

zbjornson commented 7 years ago

That probably means that your input directory isn't actually being found.

Is this the actual line that you're running:

SPADE.driver(files='input_dir', out_dir='output_dir', transforms='transforms')

If so, that means that R will look for files in a folder named "input_dir" in your working directory (run getwd() to figure out your working dir).

Usually it's easier to use a full path name, starting from (windows) the drive letter, like C:/path/to/files or (mac/linux) the root, like /users/path/to/files.

gdreiman1 commented 7 years ago

I had my working dir set to "input_dir", got it now. Thanks!