UW-GAC/GENESIS issues and pull requests

#115 - covariance between the main effect (SNP) and the interaction effect

Issue - State: open - Opened by lissettegomez 16 days ago - 1 comment

#114 - Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'saddle' not found

Issue - State: closed - Opened by ruuhsu 2 months ago - 3 comments

#113 - Available rare variant aggregate association tests

Issue - State: closed - Opened by CristianRiccio 2 months ago - 1 comment

#112 - Filter extremely small p-values by setting them to Machine$double.xmin

Pull Request - State: closed - Opened by amstilp 7 months ago

#111 - Add a helper function to calculate and filter pchisq values

Pull Request - State: closed - Opened by amstilp 7 months ago - 1 comment

#110 - Filter extreme p-values using `.Machine$double.xmin`

Issue - State: open - Opened by amstilp 7 months ago - 1 comment

#109 - Cholesky factorization failed

Issue - State: open - Opened by wangfan860 7 months ago - 1 comment

#108 - pcrelate: error with rbindlist()

Issue - State: open - Opened by AmandaHWChong 8 months ago - 1 comment

#107 - Issue: Running PCAir on 140K individuals

Issue - State: closed - Opened by AmandaHWChong 9 months ago - 1 comment

#106 - Issue with PCAir - Segmentation fault (core dumped)

Issue - State: closed - Opened by AmandaHWChong 9 months ago - 1 comment

#105 - Error using assocTestAggregate

Issue - State: open - Opened by pjuge 11 months ago - 1 comment

#104 - HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information

Issue - State: closed - Opened by GabryS3 11 months ago - 1 comment

#103 - Conditional analysis

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

#102 - High Memory Consumption with Large Dataset in PC-Relate

Issue - State: open - Opened by ecyeh about 1 year ago - 1 comment

#101 - Error when running the pcrelate function

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

#100 - ERROR:unused arguments (two.stage = TRUE, norm.option = "all", rescale = "residSD")

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

#99 - analysis pipeline for chromosome X

Issue - State: closed - Opened by candicecjj over 1 year ago - 1 comment

#98 - pcrelate REDUCE error while calculating individual AF betas

Issue - State: closed - Opened by BEFH about 2 years ago - 8 comments

#97 - add check in varCompCI that family is gaussian

Issue - State: open - Opened by smgogarten about 2 years ago

#96 - Estimate PVE

Issue - State: closed - Opened by MARCPUCV about 2 years ago - 1 comment

#95 - correctK2() drops samples under specific conditions

Issue - State: open - Opened by broomej about 2 years ago - 1 comment

#94 - enable returning the covariance matrix for GxE tests

Pull Request - State: open - Opened by mconomos over 2 years ago - 1 comment

#93 - Add burden test values to SMMAT output

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

#92 - Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE)

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

#91 - fitNullModel doesn't converge when provided a list of matrices with more than 1 matrix

Issue - State: open - Opened by tamartsi over 2 years ago - 3 comments

#90 - add fastSMMAT option and document

Pull Request - State: closed - Opened by mconomos over 2 years ago - 1 comment

#89 - bug fix for pcrelate with multiple cores

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

#88 - pcrelateToMatrix slow on 50k samples

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

#87 - Error in assocTestSingle() results when covariate is confounded with SNP genotype.

Issue - State: open - Opened by rmsegnitz over 2 years ago - 6 comments

#86 - `fitted.values` in non-mixed null models are not what we expect

Issue - State: open - Opened by amstilp over 2 years ago

#85 - Fix bug with SPA p-values for glm models

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

#84 - SPA association tests are incorrect for non-mixed models

Issue - State: closed - Opened by amstilp over 2 years ago - 1 comment
Labels: bug

#83 - bug fix: makeSparseMatrix handles numeric sample IDs

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

#82 - errors trying to use makeSparseMatrix

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

#81 - replace travis build with github actions

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

#80 - Adding functions to perform meta-analysis

Issue - State: open - Opened by marcora almost 3 years ago - 2 comments

#79 - Confusing error message in `assocTestSingle` when samples in null model are not in GDS file

Issue - State: closed - Opened by amstilp almost 3 years ago

#78 - Subset covariance matrix to samples in sample.id if specified

Pull Request - State: closed - Opened by amstilp almost 3 years ago - 4 comments

#77 - Error in assocTestSingle with Score.SPA test

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

#76 - functions for meta analysis

Pull Request - State: open - Opened by mconomos about 3 years ago

#75 - recessive and dominant coding

Pull Request - State: closed - Opened by smgogarten about 3 years ago - 2 comments

#74 - fitnullmodel error for matrix with negatives

Issue - State: closed - Opened by Reavyr about 3 years ago - 3 comments

#73 - Outdated pcair() call in vignette

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

#72 - Parallel subfn

Pull Request - State: closed - Opened by smgogarten about 3 years ago

#71 - Parallel

Pull Request - State: closed - Opened by smgogarten about 3 years ago - 3 comments

#70 - pcrelate issue for large sample size

Issue - State: closed - Opened by GraceSheng about 3 years ago - 4 comments

#69 - assocTestSingle exhausts iterators

Issue - State: closed - Opened by kaskarn over 3 years ago - 1 comment

#68 - meanImpute calculation is split into blocks for large matrices

Pull Request - State: closed - Opened by smgogarten over 3 years ago - 1 comment

#67 - Generate Dense Kinship matrix

Issue - State: closed - Opened by nkurniansyah over 3 years ago - 1 comment

#66 - Error in if (any(i < 0L)) { : missing value where TRUE/FALSE needed

Issue - State: closed - Opened by vkp3 over 3 years ago - 7 comments

#65 - updated code for recessive coding to test in association tests

Pull Request - State: closed - Opened by mchughc over 3 years ago - 1 comment

#64 - Max Number of samples for PC-AIR

Issue - State: closed - Opened by jjfarrell over 3 years ago - 13 comments

#63 - Vsif

Pull Request - State: closed - Opened by smgogarten over 3 years ago - 3 comments

#62 - variant-specific inflation factors branch

Pull Request - State: closed - Opened by tamartsi over 3 years ago - 1 comment

#61 - Issue with GxE interaction with Score test in assocTestSingle

Issue - State: closed - Opened by d1eone over 3 years ago - 1 comment

#60 - assocTestSingle results: MAC, n.obs and freq don't match.

Issue - State: closed - Opened by yangli-ai almost 4 years ago - 4 comments

#59 - Var approx v2

Pull Request - State: closed - Opened by mconomos almost 4 years ago

#58 - change use of apply in makeSparseMatrix to GENESIS:::.apply

Issue - State: closed - Opened by mchughc almost 4 years ago - 1 comment

#57 - Restructure null model

Pull Request - State: closed - Opened by amstilp almost 4 years ago - 7 comments

#56 - K0 values greater than 1

Issue - State: closed - Opened by sstadick almost 4 years ago - 1 comment

#55 - What does correctKin do?

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

#54 - change small.samp.correct default to TRUE

Pull Request - State: closed - Opened by smgogarten almost 4 years ago - 1 comment

#53 - Add error with collinear covariates

Pull Request - State: closed - Opened by amstilp almost 4 years ago - 1 comment

#52 - Small null model

Pull Request - State: closed - Opened by smgogarten almost 4 years ago - 1 comment

#51 - rename output of jointScoreTest to be consistent with assocTestSingle

Pull Request - State: closed - Opened by smgogarten almost 4 years ago - 1 comment

#50 - replace tidyverse with data.table

Pull Request - State: closed - Opened by smgogarten about 4 years ago - 2 comments

#49 - add BinomiRare and CMP tests

Pull Request - State: closed - Opened by smgogarten about 4 years ago - 3 comments

#48 - Matt branch

Pull Request - State: closed - Opened by mconomos about 4 years ago - 1 comment

#47 - parallel implementation of pcrelate

Issue - State: closed - Opened by dleopold about 4 years ago - 3 comments

#46 - varCompCI gives a heritability of 0

Issue - State: closed - Opened by yangli-ai about 4 years ago - 3 comments

#45 - Effect allele

Pull Request - State: closed - Opened by smgogarten about 4 years ago - 2 comments

#44 - Bugfix/single sample blocks

Pull Request - State: closed - Opened by sstadick about 4 years ago - 2 comments

#43 - Loss of results when doing a block comparison with a single sample in one of the blocks.

Issue - State: closed - Opened by sstadick about 4 years ago - 3 comments

#42 - Add a joint score test function

Pull Request - State: closed - Opened by amstilp about 4 years ago - 3 comments

#41 - pcrelate parallel implementation

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

#40 - fitNullModel fails if AnnotatedDataFrame contains a tibble

Issue - State: closed - Opened by smgogarten over 4 years ago - 1 comment

#39 - Force design matrices to be non-sparse

Pull Request - State: closed - Opened by amstilp over 4 years ago - 1 comment

#38 - Is it possible to test individual samples against a built model?

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

#37 - allow divergence to be NULL in pcairPartition

Pull Request - State: closed - Opened by smgogarten over 4 years ago - 2 comments

#36 - Fix issue when a starting VC is 0, or small

Pull Request - State: closed - Opened by mconomos over 4 years ago - 1 comment

#35 - added check for being a mixed model to varCompCI

Pull Request - State: closed - Opened by mconomos almost 5 years ago - 1 comment

#34 - Remove Wald from single variant and burden tests

Pull Request - State: closed - Opened by mconomos almost 5 years ago

#33 - Saige

Pull Request - State: closed - Opened by mconomos about 5 years ago - 1 comment

#32 - Carriers only tests

Pull Request - State: closed - Opened by jiwonslee about 5 years ago - 3 comments

#31 - count non missing

Pull Request - State: closed - Opened by mconomos about 5 years ago - 1 comment

#30 - bug in assocTestSingle if there are monomorphic SNPs

Issue - State: closed - Opened by jonaszierer about 5 years ago - 4 comments

#29 - PCAir unable to proceed when there are no related individuals

Issue - State: closed - Opened by seunghun23 about 5 years ago - 3 comments

#28 - error, unable to find an inherited method for function '.readSampleId' for signature

Issue - State: closed - Opened by jychungbu about 5 years ago - 9 comments

#27 - update to makeSparseMatrix to work on large matrices

Pull Request - State: closed - Opened by mconomos about 5 years ago - 5 comments

#26 - Bug with GxE when using GenotypeIterator

Issue - State: closed - Opened by jonaszierer about 5 years ago - 1 comment

#25 - MAC

Pull Request - State: closed - Opened by smgogarten about 5 years ago

#24 - variable names with "SE" or "Est" crash

Issue - State: closed - Opened by jonaszierer about 5 years ago - 1 comment

#23 - add flag of useGWG

Pull Request - State: closed - Opened by terrytianyuzhang over 5 years ago

#22 - var estimation

Pull Request - State: closed - Opened by terrytianyuzhang over 5 years ago

#21 - fastSKAT

Pull Request - State: closed - Opened by smgogarten over 5 years ago

#20 - Nullmod conv

Pull Request - State: closed - Opened by smgogarten over 5 years ago

#19 - estimating var(T) with GWG

Pull Request - State: closed - Opened by terrytianyuzhang over 5 years ago

#18 - updated kingToMatrix to account for new KING --related output

Pull Request - State: closed - Opened by mconomos over 5 years ago - 1 comment

#17 - remove redundant staff

Pull Request - State: closed - Opened by terrytianyuzhang over 5 years ago - 1 comment

#16 - PCG GENESIS first time

Pull Request - State: closed - Opened by terrytianyuzhang over 5 years ago

GitHub / UW-GAC/GENESIS issues and pull requests