Demo data: Error in `[.data.table`(y, x, nomatch = if (all.x) NA else NULL, on = by, ........

[michaelofrancis]

I am still using the provided demo data (Nalls23andMe_2019). Now I am getting an error that looks like #6 or #47 ....however the solutions provided for those issues with people's own data should not apply to the demo data. Output/error log attached with sessionInfo():

echolocatoR_log_MF_03162022.txt

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Key error output: Error in [.data.table(y, x, nomatch = if (all.x) NA else NULL, on = by, : logical error. i is not a data.table, but 'on' argument is provided. Fine-mapping complete in: Time difference of 1.8 mins [1] "+ Identifying Consensus SNPs..." [1] "++ support_thresh = 2" [1] "++ top_CS_only=FALSE" [1] "+ Calculating mean Posterior Probability (mean.PP)..." Error in [.data.table(x, r, vars, with = FALSE) : column(s) not found: SNP

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Thanks!

[michaelofrancis]

BTW, top_SNPs looking how it should. You may notice in my sessionInfo() there is no MungeSumstats but I saved top_SNPs as an R object so I could use R v4.0.5 while I figured out a different issue. Here is the whole info about top_SNPs: top_SNPs.txt

[bschilder]

This should be resolved in the echoverse branch now. Note some of the argument names have been changed/deprecated, so you can try following this new (much shorter!) vignette:

installation

remotes::install_github("RajLabMMSM/echolocatoR@echoverse")

remotes::install_github("RajLabMMSM/echolocatoR")

example

topSNPs <- echodata::topSNPs_Nalls2019
fullSS_path <- echodata::example_fullSS(dataset = "Nalls2019")

Nalls23andMe_2019.results <- echolocatoR::finemap_loci(
  fullSS_path = fullSS_path,
  topSNPs = topSNPs,
  loci = c("BST1","MEX3C"),
  dataset_name = "Nalls23andMe_2019",
  fullSS_genome_build = "hg19",
  bp_distance = 250000,
  munged = TRUE)