Reading files from Softlayer Object Storage
2
1
Entering edit mode
claudiusli ▴ 10
@claudiusli-11934
Last seen 4.8 years ago

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.

read objectstorage • 594 views
ADD COMMENT
1
Entering edit mode
@sean-davis-490
Last seen 18 days ago
United States

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 COMMENT
0
Entering edit mode
claudiusli ▴ 10
@claudiusli-11934
Last seen 4.8 years ago

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 COMMENT

Login before adding your answer.

Traffic: 338 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6