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xinhe-lab / mapgen

R package to perform gene mapping using functionally-informed genetic fine mapping
https://xinhe-lab.github.io/mapgen/
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File Reading Error In The UK LD File #10

Closed 1667857557 closed 4 months ago

1667857557 commented 4 months ago

Hi Dr.Luo We encountered an error when using the [hg19] ukb_b37_0.1_chr8.R_snp.3392926_3783017.RDS and ukb_b37_0.1_chr8.R_snp.3392926_3783017.Rvar with the code below. All files are running well except for this region.Could you provide advice on how to resolve this issue? Thank you in advance!

library(data.table)
library(mapgen)
locus<-848
LD_blocks <- readRDS(system.file('extdata', 'LD.blocks.EUR.hg19.rds', package='mapgen'))
####locus 848 <- 
###chr | start | end | locus
##8 | 3392926 | 3783017 | 848
LDREF <- load_UKBB_LDREF(LD_blocks, 
                         locus = locus, 
                         LDREF.dir = "D:/fine_mapping", 
                         prefix = "ukb_b37_0.1")

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Huang

kevinlkx commented 4 months ago

We made some updates to the finemapping functions of the package recently. You may reinstall the package and try again. Or it could be memory issue. You can try with a bigger memory.

1667857557 commented 4 months ago

Thanks for your reply,the problem has been resolved.