Ecosyste.ms: Issues

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GitHub / privefl/bigsnpr issues and pull requests

#414 - Error in if (max(abs(pred - pred0)) < 1e-06) break

Issue - State: closed - Opened by Mahantesh-Biradar almost 2 years ago - 7 comments

#413 - Running LDpred2 auto with reference sample

Issue - State: closed - Opened by lm380-r almost 2 years ago - 4 comments

#412 - Delete backing files and folders?

Issue - State: closed - Opened by Jocelyn37 almost 2 years ago - 2 comments

#411 - LD reference for HapMap3+ variants

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

#410 - Suggested model with no individual-level training data

Issue - State: closed - Opened by Fiwx almost 2 years ago - 3 comments

#409 - indexing beta_auto in per chromosome computation

Issue - State: closed - Opened by TC-gu almost 2 years ago - 7 comments

#408 - Error in { : task 1 failed - "L-BFGS-B needs finite values of 'fn'"

Issue - State: closed - Opened by Mahantesh-Biradar almost 2 years ago - 14 comments

#407 - Using own correlation matrix of LD values.

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

#406 - LDPred2 with custom reference panel

Issue - State: closed - Opened by sourena-s almost 2 years ago - 21 comments

#405 - Trouble running LDpred2-auto with a reference panel

Issue - State: closed - Opened by lm380-r almost 2 years ago - 5 comments

#404 - Question about models

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

#403 - Enable parallelism in big_counts()

Issue - State: open - Opened by privefl about 2 years ago
Labels: enhancement, good for first PR

#402 - 'bigsnpr' problem in snp_ldsc(), dependent on version 1.10.8

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

#401 - 'bigsnpr' problem in snp_cor(), dependent on version

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

#399 - Issues with LD reference in blocks

Issue - State: closed - Opened by lindseysinclair about 2 years ago - 10 comments

#397 - Give bigSNP object genotype col/row names?

Issue - State: closed - Opened by Jocelyn37 about 2 years ago - 2 comments

#396 - model saturated

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

#395 - Q about hm3 variants

Issue - State: closed - Opened by gunns2 about 2 years ago - 4 comments

#394 - snp_grid_PRS output all missing values

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

#392 - Implement matrix accessors for bed objects

Issue - State: closed - Opened by privefl about 2 years ago

#391 - Implement bed_(c)prodMat()

Issue - State: open - Opened by privefl about 2 years ago - 1 comment
Labels: good for first PR

#390 - Comparison of bigsnpr versions 1.11.4 and 1.10.8

Issue - State: closed - Opened by nathangillespie about 2 years ago - 9 comments

#389 - L-BFGS-B error

Issue - State: closed - Opened by Sabor117 about 2 years ago - 29 comments

#388 - Imputed data with HapMap3+ reference data

Issue - State: closed - Opened by Janina24 about 2 years ago - 7 comments

#387 - "long vectors not supported yet" issue when using snp_ldsplit

Issue - State: closed - Opened by cz354 about 2 years ago - 5 comments

#386 - snp_fastImpute xgboost error

Issue - State: closed - Opened by sounkou-bioinfo about 2 years ago - 3 comments

#385 - snp_readBGEN incompatible with rlang > v 1.0.0

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

#384 - Error in .sparse2g(x) : negative length vectors are not allowed

Issue - State: closed - Opened by Mahantesh-Biradar about 2 years ago - 10 comments

#382 - See if can make snp_grid_clumping() faster

Issue - State: open - Opened by privefl about 2 years ago - 1 comment
Labels: enhancement

#381 - Interpreting output of `snp_grid_clumping`

Issue - State: closed - Opened by glm729 about 2 years ago - 5 comments

#380 - missing half of SNPs after importing to bigsnpr

Issue - State: closed - Opened by xcliu-oc over 2 years ago - 3 comments

#379 - Negative h2 estimate with snp_ldsc and LDpred2 auto model selection

Issue - State: closed - Opened by xuyu-cam over 2 years ago - 3 comments

#378 - Restrict to HapMap3(+) variants / LD reference

Issue - State: closed - Opened by Smarzels over 2 years ago - 8 comments

#377 - Parallele error: object '.doSnowGlobals' not found

Issue - State: closed - Opened by YutingHan317 over 2 years ago - 2 comments

#376 - Third parameter alpha in LDpred2-auto + inference

Pull Request - State: closed - Opened by privefl over 2 years ago

#375 - NULL value returned by function snp_ldsplit

Issue - State: closed - Opened by rmehta1987 over 2 years ago - 10 comments

#374 - LDpred2-auto subset SNPs or genomewide fit?

Issue - State: closed - Opened by szhan1000 over 2 years ago - 3 comments

#373 - Run LDSC inside R with snp_ldsc?

Issue - State: closed - Opened by Ararder over 2 years ago - 3 comments

#372 - Node error on HPC when creating LD matrix

Issue - State: closed - Opened by oalavijeh over 2 years ago - 2 comments

#371 - Running tutorial across multiple chunks

Issue - State: closed - Opened by oalavijeh over 2 years ago - 14 comments

#370 - Can 'delta' be 0?

Issue - State: closed - Opened by xcyang17 over 2 years ago - 4 comments

#369 - Converting SE of OR to SE of beta

Issue - State: closed - Opened by oalavijeh over 2 years ago - 4 comments

#368 - define _FLIP_ and _REV_

Issue - State: closed - Opened by earosenthal over 2 years ago - 3 comments
Labels: enhancement, good for first PR

#367 - effect allele for LDpred scores?

Issue - State: closed - Opened by gunns2 over 2 years ago - 2 comments

#366 - How to add_code256 to data type other than 'raw' and 'unsigned char'?

Issue - State: closed - Opened by jianvhuang over 2 years ago - 2 comments

#365 - Only NAs in pred_auto

Issue - State: closed - Opened by Janina24 over 2 years ago - 2 comments

#364 - LDPred2 halts when *snp_ldsc()* is called

Issue - State: closed - Opened by jspatane over 2 years ago - 3 comments

#362 - Help understanding the output of LDpred2

Issue - State: closed - Opened by kathrynfreeman over 2 years ago - 4 comments

#361 - Error in format_snp_id(snp_id) in snp_readBGEN and snp_readBGI

Issue - State: closed - Opened by JasperHof over 2 years ago - 5 comments

#360 - Genetic correlation using LDpred2 summary statistics

Issue - State: closed - Opened by alek0991 over 2 years ago - 7 comments

#359 - Trouble getting the model performance in LDpred2

Issue - State: closed - Opened by Mahantesh-Biradar over 2 years ago - 5 comments

#358 - snp_asGeneticPos kept giving the same error message

Issue - State: closed - Opened by YunfengRuan over 2 years ago - 23 comments

#357 - Using snp_readBGEN on dnanexus RStudio server

Issue - State: closed - Opened by edobrijevic over 2 years ago - 10 comments

#356 - GWAS summary statistics from a mixed model

Issue - State: closed - Opened by alek0991 over 2 years ago - 1 comment

#355 - remove duplicates leads to index larger than maximal 46367

Issue - State: closed - Opened by AlisaBIG over 2 years ago - 8 comments

#354 - reversed sign of Beta

Issue - State: closed - Opened by alek0991 over 2 years ago - 8 comments

#353 - UKBB and hapmap3 variants

Issue - State: closed - Opened by alek0991 over 2 years ago - 4 comments

#352 - Add cross-trait LDSC

Pull Request - State: open - Opened by jean997 over 2 years ago - 9 comments

#350 - Load SFBM (.sbk) correlation matrix from disk

Issue - State: closed - Opened by alek0991 over 2 years ago - 2 comments
Labels: question

#349 - Quality control of summary statistics exclude (almost) all SNPs

Issue - State: closed - Opened by jianvhuang over 2 years ago - 9 comments

#348 - PRS coefficients

Issue - State: closed - Opened by Robbie-RL over 2 years ago - 7 comments

#347 - h2 calculated to be negative value

Issue - State: closed - Opened by AlisaBIG over 2 years ago - 2 comments

#345 - The estimated beta is all NA when using the function snp_ldpred2_grid()

Issue - State: closed - Opened by siawhui over 2 years ago - 1 comment

#344 - snp_cor() sometimes outputs values outside of [-1, 1]

Issue - State: closed - Opened by privefl over 2 years ago
Labels: bug, good for first PR

#343 - Error using snp_fastImpute

Issue - State: closed - Opened by watplatt over 2 years ago - 6 comments

#342 - How to save a .bed,.bim.,.fam set from an .rdx like object?

Issue - State: closed - Opened by watplatt over 2 years ago - 2 comments

#341 - Questions about QC Process

Issue - State: closed - Opened by jfrank94 over 2 years ago - 5 comments

#340 - Discovered outliers detected in different iterations of SVD

Issue - State: closed - Opened by fmadani over 2 years ago - 1 comment

#339 - mismatched allele1 compared to `.bed` file converted using plink2

Issue - State: closed - Opened by caimiao0714 over 2 years ago - 8 comments

#338 - heritability in function snp_simuPheno()

Issue - State: closed - Opened by Harry-Yihe-Yang over 2 years ago - 5 comments

#337 - BackingFile creation

Issue - State: closed - Opened by dzimmerman-amc over 2 years ago - 3 comments

#336 - Precision concerning bed_cprodVec

Issue - State: closed - Opened by JasmRicard over 2 years ago - 2 comments

#335 - Summary statistics comparison

Issue - State: closed - Opened by rameez500 over 2 years ago - 5 comments

#333 - NA values in the resulting correlation matrix

Issue - State: closed - Opened by alejocrojo09 almost 3 years ago - 5 comments

#323 - Settings of snp_ldsplit()

Issue - State: closed - Opened by LucieTroubat almost 3 years ago - 2 comments

#298 - Implement product that handles missing values

Issue - State: open - Opened by privefl almost 3 years ago - 1 comment
Labels: feature request

#253 - Add support for plink2 binary format dosage data (pgen)

Issue - State: open - Opened by sritchie73 over 3 years ago - 3 comments
Labels: help wanted, feature request

#238 - Computing LD correlation

Issue - State: closed - Opened by nscarene over 3 years ago - 23 comments

#219 - fix rsid-based `snp_asGeneticPos()`

Pull Request - State: closed - Opened by timo-cpr over 3 years ago - 18 comments

#202 - Error when using snp_ldsc(): Missing value where TRUE/FALSE needed.

Issue - State: closed - Opened by alovdom almost 4 years ago - 7 comments

#201 - Discard some variants in LDpred2

Issue - State: closed - Opened by privefl almost 4 years ago - 6 comments
Labels: enhancement

#200 - snp_asGeneticPos() for hg38

Issue - State: closed - Opened by JingZhang1227 almost 4 years ago - 37 comments

#176 - Support for phased data (bigHAP class)

Issue - State: closed - Opened by rborder almost 4 years ago - 10 comments

#161 - Error in snp_ldpred2_auto(): object '_bigsnpr_ldpred2_gibbs_auto' not found

Issue - State: closed - Opened by DM087 about 4 years ago - 18 comments

#147 - big_prodVec() returns NAs

Issue - State: closed - Opened by Qiaolan over 4 years ago - 5 comments

#146 - Error in calculating LD

Issue - State: closed - Opened by Qiaolan over 4 years ago - 22 comments

#124 - Error: You can't have missing values in 'X'

Issue - State: closed - Opened by May-Ibrahim over 4 years ago - 21 comments

#83 - issue with snp_asGeneticPos

Issue - State: closed - Opened by jrabino3 over 4 years ago - 30 comments

#72 - Provide progress bars using package {progressr}

Issue - State: closed - Opened by privefl almost 5 years ago - 1 comment
Labels: enhancement, feature request

#4 - Support for visualisation of LD

Issue - State: open - Opened by privefl over 7 years ago - 3 comments
Labels: feature request

#3 - Installation Error

Issue - State: closed - Opened by cbrock2 over 7 years ago - 12 comments