Interface to export LD matrix for requested region

[gaow]

Here is a feature request for an export interface that for given chr, start and end positions, a complete matrix (or sparse matrix in R which can be trivially made complete) from given blocked LD database file can be extracted.

[xiangzhu]

Thanks @gaow !

To clarify, the ideal output you need is an LD matrix for a given list of SNPs [chr pos], right? If so, I think Nick has already made some functions available along this line (but I couldn't remember the names...).

Perhaps sometimes we can also simply the input as a genomic region (e.g. gene): people only need to provide three numbers: chr, start, end.

[gaow]

Thanks @xiangzhu

Yes extracting a list of SNP is certainly of interest. But more generally (or alternatively) extraction regional LD might have interesting user case by itself. To name a couple that I can immediately think of:

1. Investigating LD structure of a genomic region of interest without a specific data-set input (list of SNPs). eg I'd like to look at what's going on in MHC region.
2. Extracting loci for fine-mapping -- these loci are obtained from literature but i'd like to try it with various other data-sets. It would be easier to just extract those loci first all at once; then for each analysis unit i'll match the exact SNPs in my data-set to get data-specific LD info. This should be faster than querying against the big database for every data-set, and also easier to share with others.