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choishingwan / choishingwan.github.io

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lassosum tutorial #1

Closed tshmak closed 4 years ago

tshmak commented 4 years ago

Hi Sam,

Thanks for doing a tutorial for lassosum on your site! Just a few suggestions on the instructions:

  1. With the newest version of lassosum, you can actually just specify LDscores = "EUR.hg19" to use the "Berisa.EUR.hg19.bed" LD regeions.
  2. You may also consider mentioning the parallel processing capabilities in the tutorial. Perhaps just refer the reader to my tutorial.

Thanks a lot!

choishingwan commented 4 years ago

Hi Tim,

Which part of the pipeline should we specify the LDscores = "EUR.hg19"? Didn't see that option in the lassosum.pipeline function.

On Thu, Aug 13, 2020 at 10:00 AM Timothy Mak notifications@github.com wrote:

Hi Sam,

Thanks for doing a tutorial for lassosum on your site! Just a few suggestions on the instructions:

  1. With the newest version of lassosum, you can actually just specify LDscores = "EUR.hg19" to use the "Berisa.EUR.hg19.bed" LD regeions.
  2. You may also consider mentioning the parallel processing capabilities in the tutorial. Perhaps just refer the reader to my tutorial.

Thanks a lot!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/choishingwan/choishingwan.github.io/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYUESUID2U5GIQ74XQDSANCMJANCNFSM4P5TLRIQ .

choishingwan commented 4 years ago

Also, double check with you:

cl <- makeCluster(2, type="FORK")

uses 2 threads, right? Based on the documentation, the 2 is specific, not nnode, which is kinda confusing. Side note: USing type="FORK" means that the multithreading won't work on windows.

On Thu, Aug 13, 2020 at 10:50 AM Shing Wan Choi choishingwan@gmail.com wrote:

Hi Tim,

Which part of the pipeline should we specify the LDscores = "EUR.hg19"? Didn't see that option in the lassosum.pipeline function.

On Thu, Aug 13, 2020 at 10:00 AM Timothy Mak notifications@github.com wrote:

Hi Sam,

Thanks for doing a tutorial for lassosum on your site! Just a few suggestions on the instructions:

  1. With the newest version of lassosum, you can actually just specify LDscores = "EUR.hg19" to use the "Berisa.EUR.hg19.bed" LD regeions.
  2. You may also consider mentioning the parallel processing capabilities in the tutorial. Perhaps just refer the reader to my tutorial.

Thanks a lot!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/choishingwan/choishingwan.github.io/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYUESUID2U5GIQ74XQDSANCMJANCNFSM4P5TLRIQ .

tshmak commented 4 years ago

As in instead of 

ld.file <- system.file("data", "Berisa.EUR.hg19.bed",package="lassosum")
ld <- fread(ld.file)
out <- lassosum.pipeline(..., LDblocks = ld)

one can simply specify, 

out <- lassosum.pipeline(..., LDblocks = "EUR.hg19")
tshmak commented 4 years ago

No, 2 is the number of nodes in makeCluster. I suppose other types than FORK may also work, but I haven't really tried.

choishingwan commented 4 years ago

Got it updated. Was wondering where this issue was located. End up finding it in my personal website, haha