r.sif: add R bigsnpr and related tools for LDpred2 analysis

[espenhgn]

Fixes #90

Changes proposed in this pull request:

• Adds additional R packages and usecase-files for LDpred2 analysis from https://github.com/comorment/ldpred2. Also, libraries imported by new R files in the deepchocolate/ldpred2 branch are present.

Note, I added the usecase files as ldpred2_tmp as I think they will be superseded by those of branch deepchocolate/ldpred2 by @deepchocolate. When they are no longer needed, they can be removed I think.
Should add that this edit only increases the size of the built container by about 100MB, from 1.4GB.

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• If this PR fixes a bug, I've added a test that will fail without my fix.
• If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

[espenhgn]

@ofrei, @deepchocolate, are you fine with this?

[ofrei]

@espenhgn looks great, thanks for including bigsnpr in R.sif!
Could you also commit into our repository the ldpred2.R and run_ldpred2.sh scripts made by @deepchocolate ? The scripts from here: 33698fb
As for impute.R, I think we could switch to plink's https://www.cog-genomics.org/plink/1.9/data#fill_missing_a2 . This options works like this:

plink --bfile <bfile_in> --fill-missing-a2 --make-bed --out <bfile_out>

[espenhgn]

Hi @ofrei. I can include @deepchocolate's files of course. If you both agree, I can merge that branch into this one and move the .R and .sh files where I want them in order to keep the contributions tracked.

[ofrei]

@espenhgn I agree

[deepchocolate]

The only thing I didn't see that I know is needed for my R-script is the R-package argparser. Otherwise it looks great!

[espenhgn]

The only thing I didn't see that I know is needed for my R-script is the R-package argparser. Otherwise it looks great!

Sorry, forgot to push this last minute change. argparser should be installed: https://github.com/comorment/containers/pull/91/files#diff-adcb955b173d581f71077f92f6a1872edb47f4f0dc61e0b23f3372a7d0dbe7fe

[espenhgn]

@deepchocolate , I just have a question: This file Height.gwas.txt referenced on line

containers/tests/ldpred2/run_ldpred2.sh

Line 6 in 33698fb

fileSumstats=Height.gwas.txt

, is that the same as this one (unzipped): https://github.com/comorment/containers/blob/deepchocolate/ldpred2/reference/examples/prsice2/Height.gwas.txt.gz?
If it's not can you push it to this branch?

[deepchocolate]

@deepchocolate , I just have a question: This file Height.gwas.txt referenced on line

containers/tests/ldpred2/run_ldpred2.sh

Line 6 in 33698fb

fileSumstats=Height.gwas.txt

, is that the same as this one (unzipped): https://github.com/comorment/containers/blob/deepchocolate/ldpred2/reference/examples/prsice2/Height.gwas.txt.gz?
If it's not can you push it to this branch?

It should be the same yes!