Genetic Risk Score (GRS) Analysis on UKB RAP

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Overview

The grs_* functions provide an end-to-end pipeline for computing and validating polygenic / genetic risk scores within the UK Biobank Research Analysis Platform (RAP). Because individual-level genotype data cannot be downloaded locally, all computationally intensive steps are executed as cloud jobs via the DNAnexus Swiss Army Knife app.

Function	Where it runs	Purpose
`grs_check()`	Local or RAP	Validate and export a SNP weights file
`grs_bgen2pgen()`	Submits RAP jobs	Convert UKB imputed BGEN files to PGEN
`grs_score()`	Submits RAP jobs	Score genotypes across chromosomes with plink2
`grs_standardize()`	Local or RAP	Z-score standardise GRS columns
`grs_zscore()`	Local or RAP	Alias for `grs_standardize()`
`grs_validate()`	Local or RAP	Assess predictive performance (OR/HR, AUC, C-index)

Typical pipeline:

grs_check()  ->  grs_bgen2pgen()  ->  grs_score()  ->  grs_standardize()  ->  grs_validate()

Prerequisite: you must be authenticated to UKB RAP and have a project selected. See vignette("auth").

Step 1: Validate the Weights File – `grs_check()`

Before uploading to RAP, validate your SNP weights file. The function reads the file, checks required columns, flags problems, and writes a plink2-compatible space-delimited output.

Required columns:

Column	Description
`snp`	SNP identifier (expected `rs` + digits format)
`effect_allele`	Effect allele: one of A / T / C / G
`beta`	Effect size (log-OR or beta); must be numeric

library(ukbflow)

# Local: weights file on your machine
w <- grs_check("weights.csv", dest = "weights_clean.txt")
#> Read 'weights.csv': 312 rows, 5 columns.
#> ✔ No NA values.
#> ✔ No duplicate SNPs.
#> ✔ All SNP IDs match rs[0-9]+ format.
#> ✔ All effect alleles are A/T/C/G.
#> Beta summary:
#>   Range     : -0.412 to 0.589
#>   Mean |beta|: 0.183
#>   Positive  : 187 (59.9%)
#>   Negative  : 125 (40.1%)
#>   Zero      : 0
#> ✔ Weights file passed checks: 312 SNPs ready for UKB RAP.
#> ✔ Saved: 'weights_clean.txt'

# On RAP (RStudio) -- use /mnt/project/ paths directly
w <- grs_check(
  file = "/mnt/project/weights/weights.csv",
  dest = "/mnt/project/weights/weights_clean.txt"
)

The validated weights are also returned invisibly for inspection.

Step 2: Convert BGEN to PGEN – `grs_bgen2pgen()`

UKB imputed genotype data is stored in BGEN format on RAP. grs_bgen2pgen() submits one Swiss Army Knife job per chromosome to convert BGEN files to the faster PGEN format with a MAF filter applied via plink2.

This function is called from your local machine or RAP RStudio – the heavy lifting runs entirely in the cloud.

# Test on the smallest chromosome first
ids <- grs_bgen2pgen(chr = 22, dest = "/pgen/", priority = "high")
#> Uploading 'grs_bgen2pgen_std.R' to RAP ...
#> ✔ Uploaded: '/grs_bgen2pgen_std.R'
#> Submitting 1 job(s) -- mem2_ssd1_v2_x4 / priority: high
#> ✔ chr22 -> 'job-Gxxxxxxxxxxxxxxxxxxxxxxxx'
#> ✔ 1/1 job(s) submitted. Monitor with job_ls().

# Full run: small chromosomes on standard, large on upgraded instance
ids_small <- grs_bgen2pgen(chr = 17:22, dest = "/pgen/")
ids_large <- grs_bgen2pgen(chr = 1:16,  dest = "/pgen/", instance = "large")

# Monitor progress (job_wait() takes one job ID at a time)
job_ls()
for (id in c(ids_small, ids_large)) job_wait(id)

Instance types:

Preset	DNAnexus instance	Cores	RAM	SSD	Recommended for
`"standard"`	`mem2_ssd1_v2_x4`	4	12 GB	200 GB	chr 15–22
`"large"`	`mem2_ssd2_v2_x8`	8	28 GB	640 GB	chr 1–16

Key arguments:

Argument	Default	Description
`chr`	`1:22`	Chromosomes to process
`dest`	—	RAP output path for PGEN files (required)
`maf`	`0.01`	MAF filter passed to plink2 `--maf`
`instance`	`"standard"`	Instance type preset
`priority`	`"low"`	Job priority (`"low"` or `"high"`)

Storage warning: chromosomes 1–16 may exceed the 200 GB SSD on "standard" instances. Use instance = "large" for these.

Step 3: Calculate GRS Scores – `grs_score()`

Once PGEN files are ready, grs_score() uploads your weights file(s) and submits one plink2 scoring job per GRS. Each job scores all 22 chromosomes and saves a single CSV to RAP.

ids <- grs_score(
  file     = c(
    grs_a = "weights/grs_a_weights.txt",
    grs_b = "weights/grs_b_weights.txt"
  ),
  pgen_dir = "/mnt/project/pgen",
  dest     = "/grs/",
  priority = "high"
)
#> ── Uploading 2 weight file(s) to RAP ────────────────────────────────────────
#> Uploading 'grs_a_weights.txt' ...
#> ✔ Uploaded: '/grs_a_weights.txt'
#> Uploading 'grs_b_weights.txt' ...
#> ✔ Uploaded: '/grs_b_weights.txt'
#> Submitting 2 job(s) -- mem2_ssd1_v2_x4 / priority: high
#> ✔ grs_a -> 'job-Gxxxxxxxxxxxxxxxxxxxxxxxx'
#> ✔ grs_b -> 'job-Gyyyyyyyyyyyyyyyyyyyyyyyy'
#> ✔ 2/2 job(s) submitted. Monitor with job_ls().

job_wait(ids)

When running from RAP RStudio with weights already at the project root, the upload step is skipped automatically:

# On RAP: weights already at /mnt/project/grs_a_weights.txt
ids <- grs_score(
  file     = c(grs_a = "/mnt/project/grs_a_weights.txt"),
  pgen_dir = "/mnt/project/pgen",
  dest     = "/grs/"
)
#> ℹ grs_a_weights.txt already at RAP root, skipping upload.

Important: the maf argument must match the value used in grs_bgen2pgen() so that the correct PGEN files are located.

Output per job: /grs/<GRS_name>_scores.csv with columns IID and the GRS score named GRS_<name>.

Step 4: Standardise GRS Columns – `grs_standardize()`

After downloading the score CSVs from RAP (via fetch_file()) and merging them into your analysis dataset, Z-score standardise each GRS column so that effect estimates are interpretable as per-SD associations.

# Auto-detect all columns containing "grs" (case-insensitive)
cohort <- grs_standardize(cohort)
#> Auto-detected 2 GRS column(s): 'GRS_a', 'GRS_b'
#> ✔ GRS_a -> GRS_a_z  [mean=0.0000, sd=1.0000]
#> ✔ GRS_b -> GRS_b_z  [mean=0.0000, sd=1.0000]

# Or specify columns explicitly
cohort <- grs_standardize(cohort, grs_cols = c("GRS_a", "GRS_b"))

grs_zscore() is an alias and produces an identical result.

The original columns are preserved; _z columns are inserted immediately after their source column.

Step 5: Validate Predictive Performance – `grs_validate()`

grs_validate() runs four complementary validation analyses for each GRS:

Analysis	What it measures
Per SD	OR (logistic) or HR (Cox) per 1-SD increase in GRS
High vs Low	OR / HR comparing top 20% vs bottom 20%
Trend test	P-trend across Q1–Q4 quartiles
Discrimination	AUC (logistic) or C-index (Cox) with 95% CI

Logistic (cross-sectional)

res <- grs_validate(
  data        = cohort,
  grs_cols    = c("GRS_a_z", "GRS_b_z"),
  outcome_col = "outcome"
)
#> ── Creating GRS groups ───────────────────────────────────────────────────────
#> ── Effect per SD (OR) ───────────────────────────────────────────────────────
#> ── High vs Low ──────────────────────────────────────────────────────────────
#> ── Trend test ───────────────────────────────────────────────────────────────
#> ── AUC ──────────────────────────────────────────────────────────────────────
#> ✔ Validation complete.

res$per_sd
res$discrimination

Cox (survival)

res <- grs_validate(
  data        = cohort,
  grs_cols    = c("GRS_a_z", "GRS_b_z"),
  outcome_col = "outcome",
  time_col    = "followup_years",
  covariates  = c("age", "sex", paste0("pc", 1:10))
)

res$per_sd          # HR per SD x model
res$high_vs_low     # HR: top 20% vs bottom 20%
res$trend           # p-trend across Q1–Q4
res$discrimination  # C-index with 95% CI

Return value: a named list with four data.table elements.

Element	Columns (logistic)	Columns (Cox)
`per_sd`	`exposure`, `term`, `model`, `OR`, `CI_lower`, `CI_upper`, `p_value`	same with `HR`
`high_vs_low`	same as `per_sd`	same with `HR`
`trend`	`exposure`, `model`, `p_trend`	same
`discrimination`	`GRS`, `AUC`, `CI_lower`, `CI_upper`	`GRS`, `C_index`, `CI_lower`, `CI_upper`

AUC calculation requires the pROC package. Install with install.packages("pROC") if needed.

Complete Pipeline Example

library(ukbflow)

# 1. Validate weights (local)
grs_check("weights.csv", dest = "weights_clean.txt")

# 2. Convert BGEN -> PGEN on RAP (submit jobs)
ids_std  <- grs_bgen2pgen(chr = 17:22, dest = "/pgen/", maf = 0.01)
ids_lrg  <- grs_bgen2pgen(chr = 1:16,  dest = "/pgen/", maf = 0.01, instance = "large")
for (id in c(ids_std, ids_lrg)) job_wait(id)

# 3. Score GRS on RAP (submit jobs)
score_ids <- grs_score(
  file     = c(grs_a = "weights_clean.txt"),
  pgen_dir = "/mnt/project/pgen",
  maf      = 0.01,   # must match grs_bgen2pgen()
  dest     = "/grs/"
)
job_wait(score_ids)

# 4. Download score CSV from RAP
fetch_file("/grs/GRS_a_scores.csv", dest = "GRS_a_scores.csv")

# 5. Merge into analysis dataset and standardise
# cohort: your analysis data.table with IID and phenotype columns
scores <- data.table::fread("GRS_a_scores.csv")   # columns: IID, GRS_a
cohort <- scores[cohort, on = "IID"]               # right-join: keep all cohort rows
cohort <- grs_standardize(cohort, grs_cols = "GRS_a")

# 6. Validate
res <- grs_validate(
  data        = cohort,
  grs_cols    = "GRS_a_z",
  outcome_col = "outcome",
  time_col    = "followup_years",
  covariates  = c("age", "sex", paste0("pc", 1:10))
)

res$per_sd
res$discrimination

Getting Help

?grs_check, ?grs_bgen2pgen, ?grs_score
?grs_standardize, ?grs_validate
vignette("auth") – RAP authentication and project selection
vignette("job") – monitoring and managing RAP jobs
vignette("assoc") – association analysis functions used inside grs_validate()
GitHub Issues

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Genetic Risk Score (GRS) Analysis on UKB RAP

Overview

Step 1: Validate the Weights File – grs_check()

Step 2: Convert BGEN to PGEN – grs_bgen2pgen()

Step 3: Calculate GRS Scores – grs_score()

Step 4: Standardise GRS Columns – grs_standardize()

Step 5: Validate Predictive Performance – grs_validate()

Logistic (cross-sectional)

Cox (survival)

Complete Pipeline Example

Getting Help

Step 1: Validate the Weights File – `grs_check()`

Step 2: Convert BGEN to PGEN – `grs_bgen2pgen()`

Step 3: Calculate GRS Scores – `grs_score()`

Step 4: Standardise GRS Columns – `grs_standardize()`

Step 5: Validate Predictive Performance – `grs_validate()`