Ecosyste.ms: Issues

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GitHub / privefl/bigsnpr issues and pull requests

#514 - How to get sample ids out of a bigsnpr object?

Issue - State: open - Opened by garyzhubc 5 months ago - 1 comment

#513 - Issue with the loop in the code

Issue - State: open - Opened by khujithrajueni 6 months ago - 3 comments

#512 - 'chi2' and 'ld_score' should have the same length

Issue - State: closed - Opened by koujiaodahan 6 months ago - 3 comments

#511 - How to deal "missing value error" on imputed genotypes data

Issue - State: open - Opened by panqinglzmc 6 months ago - 7 comments

#510 - snp_match removed ambiguous SNPs

Issue - State: closed - Opened by koujiaodahan 6 months ago - 4 comments

#509 - About the INFO value in Quality Control of GWAS summary statistics

Issue - State: open - Opened by koujiaodahan 6 months ago - 2 comments

#508 - Invalid pointer with `snp_ldsplit`

Issue - State: closed - Opened by biona001 6 months ago - 5 comments

#507 - AUC error

Issue - State: closed - Opened by alambard 6 months ago - 18 comments

#506 - how to handle ldsc with negative h2 value?

Issue - State: open - Opened by SangGold 7 months ago - 2 comments

#504 - Is it possible to call `big_univLogReg` on simulated data?

Issue - State: closed - Opened by garyzhubc 7 months ago - 1 comment

#503 - bed_projectPCA pre processing

Issue - State: closed - Opened by RoniHaas 7 months ago - 4 comments

#502 - *_autoSVD now work without call to library()

Pull Request - State: closed - Opened by dramanica 8 months ago

#501 - `snp_autoSVD()` only works after a `library("bigsnpr")` call

Issue - State: closed - Opened by dramanica 8 months ago - 4 comments

#500 - Error in makePSOCKcluster when calling snp_ldpred2_auto

Issue - State: closed - Opened by shachideshpande 8 months ago - 2 comments

#499 - scale of MCMC sampling of beta

Issue - State: closed - Opened by yidingdd 8 months ago - 3 comments

#498 - Should error when using a correlation matrix with NA / NaNs values

Issue - State: open - Opened by privefl 8 months ago
Labels: enhancement, good for first PR

#497 - Predicting phenotype after running LDpred2

Issue - State: closed - Opened by shachideshpande 8 months ago - 18 comments

#496 - Error in step #3 of projecting PC scores on new data

Issue - State: open - Opened by ozandikilitas 9 months ago - 16 comments

#495 - LDpred2: running auto model gives NAs for all beta_est

Issue - State: closed - Opened by SaraBecelaere 9 months ago - 18 comments

#494 - Handle insertions/deletions coded as I/D in snp_match()

Issue - State: open - Opened by privefl 9 months ago - 2 comments
Labels: enhancement

#493 - Would it be possible to release 1.12.6?

Issue - State: open - Opened by stefcardinale 9 months ago - 1 comment

#492 - [snp_modifyBuild] add [local.chain]

Pull Request - State: closed - Opened by Hugolyu 9 months ago - 3 comments

#491 - Getting this error while trying to convert from hg19 to hg38

Issue - State: closed - Opened by znayema 9 months ago - 8 comments

#490 - Hint for creating proper bed file from ped for polygenic risc score

Issue - State: closed - Opened by nalalenny 10 months ago - 7 comments

#489 - No $fam created with snp_readBGEN(). How to map genotype back to individuals?

Issue - State: closed - Opened by el-rs 10 months ago - 5 comments

#488 - Error when mapping file: Invalid argument.

Issue - State: closed - Opened by privefl 10 months ago - 5 comments

#487 - Script example-with-provided-LD.R does not work

Issue - State: closed - Opened by alhannae 10 months ago - 2 comments

#486 - Error when running example-with-provided-LD.R

Issue - State: closed - Opened by alhannae 10 months ago - 6 comments

#485 - Imputation for haploid organisms

Issue - State: open - Opened by adomron24 10 months ago - 2 comments

#484 - Question about LDpred2 on PRS

Issue - State: closed - Opened by wendy-xiaozong 11 months ago - 2 comments

#483 - Is it possible to plot p-values with multiple corrections?

Issue - State: closed - Opened by garyzhubc 11 months ago - 3 comments

#482 - correlation matrix

Issue - State: closed - Opened by alhannae 11 months ago - 6 comments

#480 - Error: 'chi2' should have only positive values. in snp_ldsc()

Issue - State: closed - Opened by koujiaodahan 11 months ago - 5 comments

#479 - Loading Chromosome X data (nonPAR) using bigsnpr

Issue - State: closed - Opened by JasperHof 11 months ago - 12 comments

#478 - Got only NA in calculating PRS

Issue - State: closed - Opened by KirakiraZLY 11 months ago - 10 comments

#477 - Problem with snp_match()

Issue - State: closed - Opened by girarn 11 months ago - 2 comments

#476 - Why do I get zero p-values?

Issue - State: closed - Opened by garyzhubc 11 months ago - 7 comments

#475 - Error in xtfrm.data.frame(x) : cannot xtfrm data frames

Issue - State: closed - Opened by garyzhubc 11 months ago - 1 comment

#474 - Running LDpred2 without internet server access

Issue - State: closed - Opened by uki-uiu 12 months ago - 8 comments

#473 - LDpred2-auto for EWAS

Issue - State: open - Opened by KristofferSandas about 1 year ago - 31 comments

#472 - LD calculation: NA or NAN values in the resulting correlation matrix

Issue - State: closed - Opened by JNajar about 1 year ago - 17 comments

#471 - standalone LDpred2 command line script

Issue - State: closed - Opened by espenhgn about 1 year ago - 4 comments

#470 - See if could make snp_colstats() faster

Issue - State: open - Opened by privefl about 1 year ago

#469 - Clumping option

Issue - State: closed - Opened by msong97 about 1 year ago - 4 comments

#468 - comparison of PCA from bigsnpr and PLINK

Issue - State: closed - Opened by ndimou about 1 year ago - 8 comments

#466 - Is it the correct way to annotate Manhattan plot with significance level?

Issue - State: closed - Opened by garyzhubc about 1 year ago - 3 comments

#465 - Related sample

Issue - State: closed - Opened by JuanJoMV about 1 year ago - 2 comments

#464 - Error in snp_ldsc

Issue - State: closed - Opened by KK520520 about 1 year ago - 5 comments

#463 - Error: Tested 13641 < 13641. Subscript out of bounds.

Issue - State: closed - Opened by DUAN-GAO about 1 year ago - 5 comments

#462 - EUR reference panel for GRChr38 to run LDpred2

Issue - State: closed - Opened by habraham17 about 1 year ago - 2 comments

#461 - negative heritablity result

Issue - State: closed - Opened by DUAN-GAO about 1 year ago - 3 comments

#460 - Using bigsnpr C++ headers in my package

Issue - State: open - Opened by kristjanmoore about 1 year ago - 5 comments
Labels: good for first PR

#459 - Getting started (FBM)

Issue - State: closed - Opened by DobraVila about 1 year ago - 1 comment

#457 - PCA calculation: outlier removal

Issue - State: closed - Opened by aepacker about 1 year ago - 1 comment

#456 - LD score regression, variable number of ld_size

Issue - State: closed - Opened by HerefordGuy about 1 year ago - 8 comments

#455 - Error in if (cost > max_cost) return(NULL)

Issue - State: closed - Opened by AlisaBIG over 1 year ago - 6 comments

#454 - snp_subset does not work when $fam is not there

Issue - State: closed - Opened by privefl over 1 year ago - 1 comment
Labels: bug

#453 - `Error in `db_query_fields.DBIConnection()`: ! Can't query fields.`

Issue - State: closed - Opened by garyzhubc over 1 year ago - 15 comments

#452 - Is there a way to access LD structure via bigsnpr?

Issue - State: closed - Opened by garyzhubc over 1 year ago - 5 comments

#451 - Inference with LDpred2-auto

Issue - State: closed - Opened by beradan over 1 year ago - 4 comments

#450 - Duplicate rsids

Issue - State: closed - Opened by garyzhubc over 1 year ago - 6 comments

#449 - Error running snp_readBGEN/BGI: "Wrong format of some variants"

Issue - State: closed - Opened by JasperHof over 1 year ago - 6 comments

#448 - Error in running snp_readBed

Issue - State: closed - Opened by Rui127 over 1 year ago - 3 comments

#446 - `Integer overflow` warning in `snp_cor` function

Issue - State: closed - Opened by filosi over 1 year ago - 7 comments

#445 - LDpred2: error in rowMeans on supercomputer cluster but not in R studio

Issue - State: closed - Opened by SaraBecelaere over 1 year ago - 3 comments

#444 - List of used SNPs

Issue - State: closed - Opened by AbrahamVanDeWalle almost 2 years ago - 1 comment

#443 - "NA or NaN values in the resulting correlation matrix."

Issue - State: closed - Opened by JNajar over 1 year ago - 8 comments

#442 - Question about LDpred2 Vignettes

Issue - State: closed - Opened by hrafnfaedhir about 4 years ago - 2 comments

#441 - LDpred2 PRS for one outcome?

Issue - State: closed - Opened by JNajar over 1 year ago - 3 comments

#440 - NA when running snp_ldpred2_grid

Issue - State: closed - Opened by kkleinoros over 1 year ago - 3 comments

#439 - Memory size issues in snp_cor()

Issue - State: closed - Opened by kkleinoros over 1 year ago - 10 comments

#438 - Where to get SNP IDs corresponding to LDpred2 effect sizes?

Issue - State: closed - Opened by isobel16 over 1 year ago - 6 comments

#437 - NAs with LDpred2 using UKBB and Finngen sumstats

Issue - State: closed - Opened by Herest over 1 year ago - 6 comments

#436 - Clumping without genotype data ?

Issue - State: closed - Opened by eliorzou over 1 year ago - 5 comments

#435 - Number of SNPs and their wights used for final PRS calculation

Issue - State: closed - Opened by Mahantesh-Biradar over 1 year ago - 2 comments

#434 - Integer overflow warning in snp_cor()

Issue - State: closed - Opened by fmorgante over 1 year ago - 18 comments

#433 - MCMCchain not converging

Issue - State: closed - Opened by xuxwen over 1 year ago - 7 comments

#432 - LDpred2 issue: All NAs in the final PRS file

Issue - State: closed - Opened by ShoaibBME over 1 year ago - 5 comments

#430 - `ncores` option is ignored in `snp_fastImpute`

Issue - State: closed - Opened by domiden over 1 year ago - 9 comments

#429 - Heritability

Issue - State: closed - Opened by JuanJoMV over 1 year ago - 4 comments

#428 - Re-use .sbk file

Issue - State: closed - Opened by fmorgante over 1 year ago - 6 comments

#427 - NA in LDSC

Issue - State: closed - Opened by SoleilChenxu over 1 year ago - 4 comments

#426 - Is it possible to look at the sample ids from bigsnp_obj?

Issue - State: closed - Opened by garyzhubc over 1 year ago - 2 comments

#425 - LDSC heritability

Issue - State: closed - Opened by lingjoyo over 1 year ago - 4 comments

#424 - error from : corr$add_columns(corr0, nrow(corr))

Issue - State: closed - Opened by SoleilChenxu over 1 year ago - 6 comments

#423 - LDpred2, snp_ldpred2_auto outputs NAs

Issue - State: closed - Opened by lingjoyo over 1 year ago - 3 comments

#422 - No such file: tmp-data/chr2.OMNI.interpolated_genetic_map.gz

Issue - State: closed - Opened by Deleetdk over 1 year ago - 2 comments

#421 - Inflated Q-Q

Issue - State: closed - Opened by boseb over 1 year ago - 2 comments

#420 - Unusually High h2est Values: Exceeding 1 and Reaching up to 2 or 3

Issue - State: open - Opened by PEWilliamZhou almost 2 years ago - 27 comments

#419 - Simulating multiple genetically correlated phenotypes

Issue - State: open - Opened by fmorgante almost 2 years ago - 7 comments
Labels: feature request

#418 - OpenMP flag is not passed

Issue - State: closed - Opened by barracuda156 almost 2 years ago - 1 comment

#415 - Slow running

Issue - State: closed - Opened by szhang1112 almost 2 years ago - 19 comments