Simulated Summary Statistics with LD Reference Mismatch.

Five simulated regions, each with one causal variant and 121 variants, used to illustrate how susie_rss handles a mismatch between the summary statistics and the LD reference. The first four cases simulate a phenotype from GTEx genotypes (n = 838); the last is a meta-analysis of an African-ancestry and a European-ancestry cohort.

Format

rss_mismatch_cases is a list of five cases. Each case is a list with the inputs to susie_rss:

z

z-scores.

R

LD matrix; for multi_panel, a named list of LD matrices, one per reference panel.

X

For ld_mismatch_sketch only, a genotype sketch (factor matrix) of the reference panel, used instead of R. This case also stores R, a copy of R_insample.

n

Sample size of the summary statistics.

B

Reference panel sample size, or the sketch dimension (number of rows of X), passed as R_finite; one value per panel for multi_panel. Absent for allele_flip, whose LD is in-sample.

causal

Index of the true causal variant.

The cases are:

allele_flip

In-sample LD, with the sign of the z-score reversed at 1% of the variants. Also contains z_clean, the z-scores before flipping, and flip_id, the indices of the flipped variants.

ld_mismatch

LD from 489 European individuals in 1000 Genomes.

ld_mismatch_sketch

The reference panel given as a 500-row genotype sketch X of the ADSP panel.

ser_fallback

LD from 489 European individuals in 1000 Genomes, a region where SER_fallback is TRUE.

multi_panel

Meta-analysis of 400 African-ancestry and 400 European-ancestry samples, with AFR and EUR panel LD in R. Also contains prop, the true proportion of samples from each ancestry.

ld_mismatch, ld_mismatch_sketch and ser_fallback also contain z_insample and R_insample, the z-scores and the in-sample LD on the same variants.

See also

The “Modeling and Accounting for LD Reference Mismatch in Summary Statistics Fine-mapping” vignette.

Examples

data(rss_mismatch_cases)
names(rss_mismatch_cases)
#> [1] "allele_flip"        "ld_mismatch"        "ld_mismatch_sketch"
#> [4] "ser_fallback"       "multi_panel"