This function performs univariate analysis for fine-mapping and Transcriptome-Wide Association Study (TWAS) with optional cross-validation.
Usage
univariate_analysis_pipeline(
X,
Y,
maf,
X_scalar = 1,
Y_scalar = 1,
X_variance = NULL,
other_quantities = list(),
imiss_cutoff = 1,
maf_cutoff = NULL,
xvar_cutoff = 0,
ld_reference_meta_file = NULL,
pip_cutoff_to_skip = 0,
init_L = 5,
max_L = 20,
l_step = 5,
signal_cutoff = 0.025,
coverage = c(0.95, 0.7, 0.5),
min_abs_corr = 0.8,
finemapping_extra_opts = list(refine = TRUE),
twas_weights = TRUE,
sample_partition = NULL,
max_cv_variants = -1,
cv_folds = 5,
cv_threads = 1,
verbose = 0
)Arguments
- X
A matrix of genotype data where rows represent samples and columns represent genetic variants.
- Y
A vector of phenotype measurements.
- maf
A vector of minor allele frequencies for each variant in X.
- X_scalar
A scalar or vector to rescale X to its original scale.
- Y_scalar
A scalar to rescale Y to its original scale.
- X_variance
Optional variance of X. Default is NULL.
- other_quantities
A list of other quantities to be passed to susie_post_processor. Default is an empty list.
- imiss_cutoff
Individual missingness cutoff. Default is 1.0.
- maf_cutoff
Minor allele frequency cutoff. Default is NULL.
- xvar_cutoff
Variance cutoff for X. Default is 0.05.
- ld_reference_meta_file
An optional path to a file containing linkage disequilibrium reference data. Default is NULL.
- pip_cutoff_to_skip
Cutoff value for skipping analysis based on PIP values. Default is 0.
- init_L
Initial number of components for SuSiE model optimization. Default is 5.
- max_L
The maximum number of components in SuSiE. Default is 20.
- l_step
Step size for increasing the number of components during SuSiE optimization. Default is 5.
- signal_cutoff
Cutoff value for signal identification in PIP values. Default is 0.025.
- coverage
A vector of coverage probabilities for credible sets. Default is c(0.95, 0.7, 0.5).
- min_abs_corr
Minimum absolute correlation for credible set purity filtering. Default is 0.8, which is stricter than the susieR default of 0.5.
- twas_weights
Whether to compute TWAS weights. Default is TRUE.
- sample_partition
Sample partition for cross-validation. Default is NULL.
- max_cv_variants
The maximum number of variants to be included in cross-validation. Default is -1 (no limit).
- cv_folds
The number of folds to use for cross-validation. Default is 5.
- cv_threads
The number of threads to use for parallel computation in cross-validation. Default is 1.
- verbose
Verbosity level. Default is 0.