ZikunY
commented
7 months ago Hi Shiqi,
Sorry for the late response, got super busy recently. Could you let me know if the error appeared in both annotation and no-annotations situation or if only appeared in one of it? On another note, the 1mb range in total for each loci shouldn't be the problem here.
in general, 0 and 1 should not be the problem, though CARMA would only treat it numerically rather than as a factor term. I guess, maybe the 0 and 1 input is character input? Please let me know the details so that i might be able to help here.
Still, many thanks for choosing CARMA.
Best, Zikun
Hi, I am attempting fine-mapping using CARMA, both with and without annotations. However, I have encountered a specific error :
Error in while (sum(pip[pip.order[s:length(pip.order)]]) > rho) { : missing value where TRUE/FALSE needed Calls: CARMA -> credible.set.fun.improved
I segmented the loci based on the 500kb regions upstream and downstream of the primary SNP, which resulted in some loci with a relatively small number of SNPs. I'm not sure if this is the reason? Do you know what is going on here and how I can troubleshoot? Furthermore, my annotations consist of a binary variable with values 0 or 1. Could this impact the results obtained from CARMA?
My code: CARMA.results<-CARMA(z.list,ld.list,lambda.list=lambda.list,outlier.switch=F) CARMA.results<-CARMA(z.list,ld.list,lambda.list=lambda.list,w.list=annot.list,outlier.switch=F)
Matrix products: default BLAS/LAPACK: /p300s/biosoft/app/python/python2023/envs/R4.3.1/lib/libopenblasp-r0.3.23.so; LAPACK version 3.11.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] R.utils_2.12.2 R.oo_1.25.0 R.methodsS3_1.8.2 devtools_2.4.5 [5] usethis_2.2.2 dplyr_1.1.2 magrittr_2.0.3 data.table_1.14.8 [9] CARMA_1.0
loaded via a namespace (and not attached): [1] utf8_1.2.3 generics_0.1.3 shape_1.4.6 stringi_1.7.12 [5] lattice_0.21-8 digest_0.6.33 grid_4.3.1 iterators_1.0.14 [9] pkgload_1.3.2.1 fastmap_1.1.1 foreach_1.5.2 glmnet_4.1-7 [13] Matrix_1.6-0 processx_3.8.2 sessioninfo_1.2.2 pkgbuild_1.4.2 [17] survival_3.5-5 urlchecker_1.0.1 ps_1.7.5 promises_1.2.0.1 [21] purrr_1.0.1 fansi_1.0.4 codetools_0.2-19 cli_3.6.1 [25] shiny_1.7.4.1 rlang_1.1.1 crayon_1.5.2 ellipsis_0.3.2 [29] splines_4.3.1 remotes_2.4.2.1 cachem_1.0.8 tools_4.3.1 [33] memoise_2.0.1 httpuv_1.6.11 vctrs_0.6.3 R6_2.5.1 [37] mime_0.12 lifecycle_1.0.3 stringr_1.5.0 htmlwidgets_1.6.2 [41] fs_1.6.3 MASS_7.3-60 miniUI_0.1.1.1 pkgconfig_2.0.3 [45] callr_3.7.3 pillar_1.9.0 later_1.3.1 profvis_0.3.8 [49] glue_1.6.2 Rcpp_1.0.11 tibble_3.2.1 tidyselect_1.2.0 [53] xtable_1.8-4 htmltools_0.5.5 compiler_4.3.1 prettyunits_1.1.1