Requirements

Y sample order and pgen sample order (as defined in .psam for plink2 files or .fam for plink1 files) should match. All coordinates are in hg19. We will harmonize weights and GWAS genotype data internally.

Prepare input

library(ctwas)
# phenotype
data(Y)

# individual level genotype data
pgenfs <- system.file("extdata/example_genotype_files", paste0("example_chr", 1:22, ".pgen"), package = "ctwas")

# weight
weight.fusion <- system.file("extdata/example_fusion_weights", "Tissue", package = "ctwas")

or predict weight

weight.predictdb <- system.file("extdata", "example_tissue.db", package = "ctwas") 

Impute expression

outputdir <- "~/temp"

exprfs <- impute_expr(pgenfs = pgenfs, weight = weight.fusion,
                           method = "lasso", outputdir = outputdir,
                           outname = "test")
#> 2021-06-06 20:19:15 INFO::Harmonize set to True: will flip weights to match LD reference
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 1: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 1
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 1.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 2: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 2
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 2.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 3: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 3
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 3.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 4: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 4
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 4.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 5: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 5
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 5.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 6: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 6
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 6.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 7: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 7
#> 2021-06-06 20:19:16 INFO::expression inmputation done for chr 7.
#> 2021-06-06 20:19:16 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:16 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:16 INFO::number of genes on chromosome 8: 1
#> 2021-06-06 20:19:16 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:16 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:16 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:16 INFO::Number of genes with imputed expression: 1 for chr 8
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 8.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 9: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 9
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 9.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 10: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 10
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 10.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 11: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 11
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 11.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 12: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 12
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 12.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 13: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 13
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 13.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 14: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 14
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 14.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 15: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 15
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 15.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 16: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 16
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 16.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 17: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 17
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 17.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 18: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 18
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 18.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 19: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 19
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 19.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 20: 1
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Start gene z score imputation ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 1 for chr 20
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 20.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 21: 0
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 0 for chr 21
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 21.
#> 2021-06-06 20:19:17 INFO::Reading weights for chromosome
#> 2021-06-06 20:19:17 INFO::number of genes with weights provided: 20
#> 2021-06-06 20:19:17 INFO::number of genes on chromosome 22: 0
#> 2021-06-06 20:19:17 INFO::collecting gene weight information ...
#> 2021-06-06 20:19:17 INFO::Imputation done, writing results to output...
#> 2021-06-06 20:19:17 INFO::Number of genes with imputed expression: 0 for chr 22
#> 2021-06-06 20:19:17 INFO::expression inmputation done for chr 22.

Run ctwas

regionsfile <- system.file("extdata", "example_regions.bed", package = "ctwas")

ctwas(pgenfs, exprfs, Y, ld_regions_custom = regionsfile, thin = 1, max_snp_region = 20, outputdir = outputdir, outname = "test", ncore = 1)
#> 2021-06-06 20:19:17 INFO::ctwas started ...
#> 2021-06-06 20:19:17 INFO::LD region file: /tmp/RtmpzZjoXP/temp_libpath6eb4bb559ef/ctwas/extdata/example_regions.bed
#> 2021-06-06 20:19:17 INFO::No. LD regions: 374
#> 2021-06-06 20:19:17 INFO::No. regions with at least one SNP/gene for chr1: 17
#> 2021-06-06 20:19:17 INFO::Merge regions for chr1
#> 2021-06-06 20:19:17 INFO::No. regions with at least one SNP/gene for chr1 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr2: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr2
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr2 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr3: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr3
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr3 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr4: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr4
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr4 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr5: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr5
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr5 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr6: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr6
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr6 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr7: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr7
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr7 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr8: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr8
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr8 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr9: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr9
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr9 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr10: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr10
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr10 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr11: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr11
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr11 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr12: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr12
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr12 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr13: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr13
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr13 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr14: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr14
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr14 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr15: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr15
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr15 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr16: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr16 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr17: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr17 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr18: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr18
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr18 after merging: 16
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr19: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr19
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr19 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr20: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr20
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr20 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr21: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr21
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr21 after merging: 17
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr22: 17
#> 2021-06-06 20:19:18 INFO::Merge regions for chr22
#> 2021-06-06 20:19:18 INFO::No. regions with at least one SNP/gene for chr22 after merging: 17
#> 2021-06-06 20:19:18 INFO::Trim regions with SNPs more than Inf
#> 2021-06-06 20:19:18 INFO::Run susie iteratively, getting rough estimate ...
#> 2021-06-06 20:19:18 INFO::run iteration 1
#> 2021-06-06 20:19:31 INFO::After iteration 1, gene prior 0.148775562964219:, SNP prior:0.0338114658847404
#> 2021-06-06 20:19:31 INFO::run iteration 2
#> 2021-06-06 20:19:41 INFO::After iteration 2, gene prior 0.0891262303945526:, SNP prior:0.0331128445182952
#> 2021-06-06 20:19:41 INFO::run iteration 3
#> 2021-06-06 20:19:51 INFO::After iteration 3, gene prior 0.0681251887491905:, SNP prior:0.0328810571688283
#> 2021-06-06 20:19:52 INFO::Blocks are filtered: 11 blocks left
#> 2021-06-06 20:19:52 INFO::Run susie iteratively, getting accurate estimate ...
#> 2021-06-06 20:19:52 INFO::run iteration 1
#> 2021-06-06 20:19:55 INFO::After iteration 1, gene prior 0.121302748556619:, SNP prior:0.0246458256410007
#> 2021-06-06 20:19:55 INFO::run iteration 2
#> 2021-06-06 20:19:56 INFO::After iteration 2, gene prior 0.127950835442531:, SNP prior:0.0222724471155796
#> 2021-06-06 20:19:56 INFO::run iteration 3
#> 2021-06-06 20:19:57 INFO::After iteration 3, gene prior 0.129420982680997:, SNP prior:0.0210827655543845
#> 2021-06-06 20:19:57 INFO::run iteration 4
#> 2021-06-06 20:19:58 INFO::After iteration 4, gene prior 0.129780331696682:, SNP prior:0.0203569154265732
#> 2021-06-06 20:19:58 INFO::run iteration 5
#> 2021-06-06 20:19:59 INFO::After iteration 5, gene prior 0.129885153950325:, SNP prior:0.0198667579184352
#> 2021-06-06 20:19:59 INFO::run iteration 6
#> 2021-06-06 20:20:00 INFO::After iteration 6, gene prior 0.12992813995828:, SNP prior:0.019515764837907
#> 2021-06-06 20:20:00 INFO::run iteration 7
#> 2021-06-06 20:20:01 INFO::After iteration 7, gene prior 0.129953766169702:, SNP prior:0.0192551545567027
#> 2021-06-06 20:20:01 INFO::run iteration 8
#> 2021-06-06 20:20:02 INFO::After iteration 8, gene prior 0.129972850513127:, SNP prior:0.0190571803189086
#> 2021-06-06 20:20:02 INFO::run iteration 9
#> 2021-06-06 20:20:03 INFO::After iteration 9, gene prior 0.129988408195503:, SNP prior:0.0189047073031786
#> 2021-06-06 20:20:03 INFO::run iteration 10
#> 2021-06-06 20:20:04 INFO::After iteration 10, gene prior 0.130001545526375:, SNP prior:0.0187864992402113
#> 2021-06-06 20:20:04 INFO::run iteration 11
#> 2021-06-06 20:20:05 INFO::After iteration 11, gene prior 0.130012831938942:, SNP prior:0.0186948415727503
#> 2021-06-06 20:20:05 INFO::run iteration 12
#> 2021-06-06 20:20:06 INFO::After iteration 12, gene prior 0.130022638918744:, SNP prior:0.0186242408849974
#> 2021-06-06 20:20:06 INFO::run iteration 13
#> 2021-06-06 20:20:08 INFO::After iteration 13, gene prior 0.130031237254361:, SNP prior:0.0185706670676291
#> 2021-06-06 20:20:08 INFO::run iteration 14
#> 2021-06-06 20:20:09 INFO::After iteration 14, gene prior 0.13003883375891:, SNP prior:0.0185310890917328
#> 2021-06-06 20:20:09 INFO::run iteration 15
#> 2021-06-06 20:20:10 INFO::After iteration 15, gene prior 0.130045590104124:, SNP prior:0.0185031787529345
#> 2021-06-06 20:20:10 INFO::run iteration 16
#> 2021-06-06 20:20:11 INFO::After iteration 16, gene prior 0.130051634646391:, SNP prior:0.018485115006774
#> 2021-06-06 20:20:11 INFO::run iteration 17
#> 2021-06-06 20:20:12 INFO::After iteration 17, gene prior 0.130057070586389:, SNP prior:0.0184754508987925
#> 2021-06-06 20:20:12 INFO::run iteration 18
#> 2021-06-06 20:20:13 INFO::After iteration 18, gene prior 0.130061981833586:, SNP prior:0.0184730207419806
#> 2021-06-06 20:20:13 INFO::run iteration 19
#> 2021-06-06 20:20:14 INFO::After iteration 19, gene prior 0.130066437311989:, SNP prior:0.0184768739176472
#> 2021-06-06 20:20:14 INFO::run iteration 20
#> 2021-06-06 20:20:15 INFO::After iteration 20, gene prior 0.13007049416891:, SNP prior:0.0184862267311746
#> 2021-06-06 20:20:15 INFO::run iteration 21
#> 2021-06-06 20:20:16 INFO::After iteration 21, gene prior 0.130074200196718:, SNP prior:0.0185004267842584
#> 2021-06-06 20:20:16 INFO::run iteration 22
#> 2021-06-06 20:20:17 INFO::After iteration 22, gene prior 0.130077595682047:, SNP prior:0.0185189261960064
#> 2021-06-06 20:20:17 INFO::run iteration 23
#> 2021-06-06 20:20:18 INFO::After iteration 23, gene prior 0.130080714833321:, SNP prior:0.0185412611910075
#> 2021-06-06 20:20:18 INFO::run iteration 24
#> 2021-06-06 20:20:19 INFO::After iteration 24, gene prior 0.130083586894162:, SNP prior:0.0185670363418959
#> 2021-06-06 20:20:19 INFO::run iteration 25
#> 2021-06-06 20:20:20 INFO::After iteration 25, gene prior 0.130086237020213:, SNP prior:0.0185959122638647
#> 2021-06-06 20:20:20 INFO::run iteration 26
#> 2021-06-06 20:20:21 INFO::After iteration 26, gene prior 0.130088686975932:, SNP prior:0.0186275959030792
#> 2021-06-06 20:20:21 INFO::run iteration 27
#> 2021-06-06 20:20:22 INFO::After iteration 27, gene prior 0.130090955693026:, SNP prior:0.0186618327977587
#> 2021-06-06 20:20:22 INFO::run iteration 28
#> 2021-06-06 20:20:23 INFO::After iteration 28, gene prior 0.130093059721574:, SNP prior:0.0186984008561063
#> 2021-06-06 20:20:23 INFO::run iteration 29
#> 2021-06-06 20:20:24 INFO::After iteration 29, gene prior 0.130095013597163:, SNP prior:0.0187371053125042
#> 2021-06-06 20:20:24 INFO::run iteration 30
#> 2021-06-06 20:20:25 INFO::After iteration 30, gene prior 0.13009683014178:, SNP prior:0.0187777746076048
#> 2021-06-06 20:20:25 INFO::Run susie for all regions.
#> 2021-06-06 20:20:25 INFO::run iteration 1
#> 2021-06-06 20:20:43 INFO::After iteration 1, gene prior 0.121047368537169:, SNP prior:0.0914181878021201
#> $group_prior
#> [1] 0.13009683 0.01877777
#> 
#> $group_prior_var
#> [1] 0.2032782542 0.0002760492
sessionInfo()
#> R version 3.6.1 (2019-07-05)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Scientific Linux 7.4 (Nitrogen)
#> 
#> Matrix products: default
#> BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
#> 
#> 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       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] ctwas_0.1.28
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.5        compiler_3.6.1    pillar_1.5.1     
#>  [4] iterators_1.0.10  tools_3.6.1       digest_0.6.20    
#>  [7] debugme_1.1.0     evaluate_0.14     memoise_1.1.0    
#> [10] lifecycle_1.0.0   tibble_3.1.0      lattice_0.20-38  
#> [13] pkgconfig_2.0.2   rlang_0.4.10      Matrix_1.2-18    
#> [16] foreach_1.4.4     DBI_1.1.0         parallel_3.6.1   
#> [19] yaml_2.2.0        pkgdown_1.6.1     xfun_0.8         
#> [22] stringr_1.4.0     dplyr_1.0.5       knitr_1.23       
#> [25] pgenlibr_0.2      desc_1.2.0        generics_0.0.2   
#> [28] fs_1.3.1          vctrs_0.3.7       tidyselect_1.1.0 
#> [31] rprojroot_1.3-2   grid_3.6.1        glue_1.4.2       
#> [34] data.table_1.13.2 R6_2.4.0          fansi_0.4.0      
#> [37] rmarkdown_1.13    purrr_0.3.4       magrittr_1.5     
#> [40] backports_1.1.4   codetools_0.2-16  htmltools_0.3.6  
#> [43] ellipsis_0.2.0.1  assertthat_0.2.1  logging_0.10-108 
#> [46] utf8_1.1.4        stringi_1.4.3     doParallel_1.0.14
#> [49] crayon_1.3.4