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Loads weights in PredictDB or FUSION format

Source: R/ctwas_weights.R
load_weights.Rd

Loads weights in PredictDB or FUSION format

Usage

load_weights(
  weight_file,
  weight_format = c("PredictDB", "FUSION"),
  filter_protein_coding_genes = TRUE,
  load_predictdb_LD = TRUE,
  fusion_method = c("lasso", "enet", "top1", "blup", "bslmm", "best.cv"),
  fusion_genome_version = NA,
  ncore = 1
)

Arguments

weight_file

filename of the '.db' file for PredictDB weights; or the directory containing '.wgt.RDat' files for FUSION weights.

weight_format

a string or a vector, specifying format of each weight file, e.g. PredictDB, FUSION.

filter_protein_coding_genes

If TRUE, keep protein coding genes only. This option is only for PredictDB weights

load_predictdb_LD

If TRUE, load pre-computed LD among weight SNPs. This option is only for PredictDB weights

fusion_method

a string, specifying the method to choose in FUSION models. "best.cv" option will use the best model (smallest p-value) under cross-validation.

fusion_genome_version

a string, specifying the genome version of FUSION models

ncore

integer, number of cores for parallel computing.