UW-GAC/GENESIS

Issues

• how to check the assumption of poisson regression

  #117 opened 2 months ago by yu-zhang-oYo
  0

• NA values in results of assocTestSingle

  #116 opened 3 months ago by yu-zhang-oYo
  7

• covariance between the main effect (SNP) and the interaction effect

  #115 opened 3 months ago by lissettegomez
  1

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

  #114 opened 5 months ago by ruuhsu
  3

• Available rare variant aggregate association tests

  #113 opened 5 months ago by CristianRiccio
  1

• Error when running the pcrelate function

  #101 opened 2 years ago by AmandaHWChong
  3

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

  #110 opened 10 months ago by amstilp
  1

• Cholesky factorization failed

  #109 opened 10 months ago by wangfan860
  1

• pcrelate: error with rbindlist()

  #108 opened a year ago by AmandaHWChong
  1

• Issue: Running PCAir on 140K individuals

  #107 opened a year ago by AmandaHWChong
  1

• Issue with PCAir - Segmentation fault (core dumped)

  #106 opened a year ago by AmandaHWChong
  1

• Error using assocTestAggregate

  #105 opened a year ago by pjuge
  1

• Error in assocTestSingle with Score.SPA test

  #77 opened 3 years ago by ZeyuanSong
  3

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

  #104 opened a year ago by GabryS3
  1

• Conditional analysis

  #103 opened a year ago by angelosarmen
  1

• High Memory Consumption with Large Dataset in PC-Relate

  #102 opened a year ago by ecyeh
  1

• Estimate PVE

  #96 opened a year ago by MARCPUCV
  1

• pcrelateToMatrix slow on 50k samples

  #88 opened a year ago by byoo
  10

• Error in assocTestSingle() results when covariate is confounded with SNP genotype.

  #87 opened 3 years ago by rmsegnitz
  6

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

  #100 opened 2 years ago by DamienTan
  2

• analysis pipeline for chromosome X

  #99 opened 2 years ago by candicecjj
  1

• correctK2() drops samples under specific conditions

  #95 opened 2 years ago by broomej
  1

• pcrelate REDUCE error while calculating individual AF betas

  #98 opened 2 years ago by BEFH
  8

• add check in varCompCI that family is gaussian

  #97 opened 2 years ago by smgogarten
  0

• Error in seqVCF2GDS(vcf.files, gds.file, verbose = FALSE)

  #92 opened 3 years ago by Bulouere
  1

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

  #91 opened 3 years ago by tamartsi
  3

• fitnullmodel error for matrix with negatives

  #74 opened 3 years ago by Reavyr
  3

• Confusing error message in `assocTestSingle` when samples in null model are not in GDS file

  #79 opened 3 years ago by amstilp
  0

• SPA association tests are incorrect for non-mixed models

  #84 opened 3 years ago by amstilp
  1

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

  #86 opened 3 years ago by amstilp
  0

• errors trying to use makeSparseMatrix

  #82 opened 3 years ago by earosenthal
  5

• Adding functions to perform meta-analysis

  #80 opened 3 years ago by marcora
  2

• parallel implementation of pcrelate

  #47 opened 3 years ago by dleopold
  3

• assocTestSingle exhausts iterators

  #69 opened 3 years ago by kaskarn
  1

• Outdated pcair() call in vignette

  #73 opened 3 years ago by pamelarussell
  2

• pcrelate issue for large sample size

  #70 opened 3 years ago by GraceSheng
  4

• change use of apply in makeSparseMatrix to GENESIS:::.apply

  #58 opened 3 years ago by mchughc
  1

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

  #66 opened 3 years ago by vkp3
  7

• Max Number of samples for PC-AIR

  #64 opened 3 years ago by jjfarrell
  13

• Generate Dense Kinship matrix

  #67 opened 4 years ago by nkurniansyah
  1

• Issue with GxE interaction with Score test in assocTestSingle

  #61 opened 4 years ago by d1eone
  1

• assocTestSingle results: MAC, n.obs and freq don't match.

  #60 opened 4 years ago by yangli-ai
  4

• varCompCI gives a heritability of 0

  #46 opened 4 years ago by yangli-ai
  3

• K0 values greater than 1

  #56 opened 4 years ago by sstadick
  1

• Is it possible to test individual samples against a built model?

  #38 opened 5 years ago by sstadick
  5

• What does correctKin do?

  #55 opened 4 years ago by sstadick
  4

• fitNullModel fails if AnnotatedDataFrame contains a tibble

  #40 opened 4 years ago by smgogarten
  1

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

  #43 opened 4 years ago by sstadick
  3

• pcrelate parallel implementation

  #41 opened 5 years ago by dleopold
  2

• bug in assocTestSingle if there are monomorphic SNPs

  #30 opened 5 years ago by jonaszierer
  4