finemap_regress: Fine-mapping and clustering SEs with SUR

In bhattacharya-a-bt/isoTWAS: Isoform-level transcriptome-wide association studies

Fine-mapping and clustering SEs with SUR

Description

The function feature selects with SuSiE and runs SUR with cluster-robust SEs

Usage

finemap_regress(
  X,
  Y,
  Y.rep,
  R,
  id,
  verbose = F,
  tx_names = NULL,
  coverage = 0.9
)

Arguments

X	matrix, design matrix of SNP dosages
Y	matrix, matrix of G mean isoform expression across columns
Y.rep	matrix, matrix of G isoform expression with replicates
R	int, number of replicates
id	vector, vector of sample ids showing rep to id
verbose	logical
tx_names	vector, character vector of tx names in order of columns of Y
coverage	numeric, coverage of credible set

Value

data frame of elastic net, lasso, and LMM based predictions

bhattacharya-a-bt/isoTWAS documentation built on Jan. 9, 2025, 10:25 p.m.