Reasoning behind matching of IDs #1

[scienception]

Referring to file: code/example-with-provided-LD.R
in which case ind.chr3 and ind.chr2 are not the same?

## indices in 'df_beta'
ind.chr <- which(df_beta$chr == chr)
## indices in 'map_ldref'
ind.chr2 <- df_beta$`_NUM_ID_`[ind.chr]
## indices in 'corr_chr'
ind.chr3 <- match(ind.chr2, which(map_ldref$chr == chr))

'df_beta' was derived from this matching:
(info_snp <- tibble::as_tibble(snp_match(sumstats, map_ldref, return_flip_and_rev = T))), so it already contains the variants that are both in the summary statistics and map_ldref, as well as the right chromosome (which(df_beta$chr == chr)). So not sure what ind.chr3 <- match(ind.chr2, which(map_ldref$chr == chr)) is doing here.

[privefl]

What would you use instead?

[scienception]

I believe ind.chr2 <- df_beta$_NUM_ID_[ind.chr] already contains the same info as ind.chr3.
Since you already filter for the specific chromosome you need and you take the indices of map_ldref from _NUM_ID_ column.

[privefl]

I don't follow you.
ind.chr3 is needed to get the subset of each LD matrix (the indices relative to each chromosome).
Using ind.chr2 instead of ind.chr3 wouldn't work.