Error with genome build of the reference

[swvanderlaan]

Hi,

Just running your example lines to test the installation. See below:

library(HOPS)
data(UKBiobank_ZscoresSubset)
ZscoreMatrixWhitened_UKBB <- GetWhitenedZscores(ZscoreMatrix = ZscoreMatrix_UKBB, ZscoreCorMatrix = ZscoreCorMatrix_UKBB)
HOPS_UKBB <- GetHOPS(ZscoreWhitenedMatrix = ZscoreMatrixWhitened_UKBB, RSids = SNPinfo_UKBB$SNPid, LDCorrected = TRUE, POLYGENICITYCorrected = FALSE, GlobalTest = TRUE)
using LD scores from https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_baseline_v1.1_ldscores.tgz
Warning messages:
1: In GetHOPS(ZscoreWhitenedMatrix = ZscoreMatrixWhitened_UKBB, RSids = SNPinfo_UKBB$SNPid,  :
  Matching LD scores on RSids, please make sure the SNPs are in build 38.

2: In GetHOPS(ZscoreWhitenedMatrix = ZscoreMatrixWhitened_UKBB, RSids = SNPinfo_UKBB$SNPid,  :
  0% of the SNPs will not be scored because of lacking LD scores.

How could I fix the genome build of the reference? Is there another link (than this one: https://data.broadinstitute.org/alkesgroup/LDSCORE/1000G_Phase3_baseline_v1.1_ldscores.tgz) that could be used?

Thanks!

Sander

[marieverbanck]

Hi Sander,
sorry, this was simply meant to be a warning (not an error) but it should have said build 37 instead of 38. I will fix it. This link to LD scores is the correct one.
As for the second warning, I'll add a condition on that, it shouldn't be printed unless the percentage of unscored SNPs is > 0%.
Thank you very much for mentioning it.
I hope this is clear.
Best,
Marie