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Question: Reading files from Softlayer Object Storage
1
gravatar for claudiusli
11 months ago by
claudiusli10
claudiusli10 wrote:

I'm trying to read in files that I have sitting on Softlayer's Object Storage.

This library https://github.com/IBMDataScience/objectStoreR lets you pull in a CSV files as data frames.

It's seems easy to modify it to just read it in as raw data but I'm not sure how to get that into flowcore.

read.FCS seems like the logical place to look but that expects a local file.

 

Very new to R, bioconductor and object storag so any pointers on the where to start looking for this would be apprecaited.

ADD COMMENTlink modified 11 months ago • written 11 months ago by claudiusli10

https://github.com/IBMDataScience/objectStoreR/issues/2

ADD REPLYlink written 11 months ago by Sean Davis21k
1
gravatar for Sean Davis
11 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

The objectStoreR package is VERY specific in that it only deals with CSV files. As a simple starting place, you could contact the author and ask if he/she is willing to write a objectstore.fetchToDisk() function that simply grabs an object and writes it to disk.  That would allow you to interface with the vast majority of R I/O functions.  Alternatively, you could modify the current get() function to save to disk.  The GET() call is the place to make changes, most likely.

ADD COMMENTlink written 11 months ago by Sean Davis21k
0
gravatar for claudiusli
11 months ago by
claudiusli10
claudiusli10 wrote:

Yeah. I thought about doing that but it seems like a messy solution.

I was hoping that I could either modify objectStoreR to provide the data in a manner palatable to flowCore or that there was some other way to populate a flowFrame from data in memory.

I'll look into modifying objectStoreR as you suggested.

ADD COMMENTlink written 11 months ago by claudiusli10
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