Imputing z-statistics
An example analysis
Developed by Gabriel Hoffman
Run on 2025-07-28 10:48:40.287666
Source:vignettes/imputez.Rmd
imputez.RmdThe imputez package uses GenomicDataStream
to read genetic data from a reference panel. Here, simulate z-statstics
and use run_imputez() to perform the imputation.
Code
library(imputez)
library(GenomicDataStream)
library(mvtnorm)
library(dplyr)
# VCF file for reference
file <- system.file("extdata", "test.vcf.gz", package = "GenomicDataStream")
# initialize data stream
gds = GenomicDataStream(file, "DS", initialize=TRUE)
# read genotype data from reference
dat = getNextChunk(gds)
# simulate z-statistics with correlation structure
# from the LD of the reference panel
z = c(rmvnorm(1, rep(0, 10), cor(dat$X)))
# Combine z-statistics with variant ID, position, etc
df = dat$info %>%
mutate(z = z, GWAS_A1 = A1, GWAS_A2 = A2) %>%
rename(REF_A1 = A1, REF_A2 = A2)
# Given observed z-statistics and
# GenomicDataStream of reference panel,
# Impute z-statistics from variants missing z-statistics.
# Here drop variant 2, and then impute its z-statistic
# Defaults to run imputezDecorr / decorrelate in the backend
res = run_imputez(df[-2,], gds, 10000, 1000)
# Results of imputed z-statistics
res## # A tibble: 1 × 9
## ID A1 A2 z.stat se r2.pred lambda maf nVariants
## <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int>
## 1 1:11000:T:C T C 0.0000602 0.0000291 8.45e-10 1.00 0.0159 9Session Info
## R version 4.4.2 (2024-10-31)
## Platform: aarch64-apple-darwin23.6.0
## Running under: macOS Sonoma 14.7.1
##
## Matrix products: default
## BLAS: /Users/gabrielhoffman/prog/R-4.4.2/lib/libRblas.dylib
## LAPACK: /opt/homebrew/Cellar/r/4.4.3_1/lib/R/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
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## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] dplyr_1.1.4 mvtnorm_1.3-3 GenomicDataStream_0.0.17
## [4] Rdpack_2.6.2 progress_1.2.3 Rcpp_1.0.14
## [7] imputez_1.2.2 BiocStyle_2.34.0
##
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