LDpred2: LD window, imputation,etc

[deepchocolate]

Is your feature request related to a problem? Please describe.
These are just some modifications of the LDpred2 R-scripts discussed in #117 and elsewhere.

Imputation: The current version of LDpred2.R will impute genotypes each time it is run. It would be better to move the imputation step to createBackingFile.R as the imputation step takes a significant amount of time. Solved by usecases/LDpred2/imputeGenotypes.R

SNP window for LD: calculateLD.R only accepts a window defined in centimorgans. As suggested by @ofrei it would be good to let the user specify this window in centimorgans, basepairs or SNP index.

Tutorial: Add some more details regarding arguments such as --col-snp-id and improve error output to point out to user how to solve an error if possible.

Matching genotype and sumstats: snp_match can match using CHR, A0, A1 and one of BP or RSID. ldpred2.R currently throws an error if any of them are not available. Fixed

Minor discussion point: The createBackingFile.R could probably be renamed to something more informative. It creates two files, and it specifically only works with bed-files as input. Maybe convertBedToBigSNPR.R or convertBedToRDS.R. The latter rhymes better with the arguments to calculateLD.R and ldpred2.R as the input genotype file is placed in flag --geno-file-rds. (The .bk holds the actual data and the .rds-file is meta data unless I missed something.)

Various
This condition seems to have no purpose at the moment. Since --chr2use has a default it should probably always run.

containers/usecases/LDpred2/ldpred2.R

Lines 183 to 189 in b984ff6

	if (TRUE) {
	cat('Filtering SNPs based on --chr2use\n')
	nSNPsBefore <- nrow(sumstats)
	sumstats <- sumstats[sumstats$chr %in% chr2use,]
	nSNPsAfter <- nrow(sumstats)
	cat('Retained', nSNPsAfter, 'out of', nSNPsBefore,'\n')
	}

Fixed

Describe the solution you'd like

• Move genotype imputation from LDpred2.R to createBackingFile.R
• Add options for type of window to use in calculateLD.R. We add flags for --ld-window-snps (SNPs raw index in .bim file), --ld-window-kb (distance in kilobase pairs, BP column in .bim file), and --ld-window-cm (current use with --window, GP column in .bim file). The user should only be able to specify one of these options.
• Potentially change the name of createBackingFile.R

Describe alternatives you've considered
None

Additional context
None

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