NAMESPACE

exportPattern("^[[:alpha:]]+")
import(Rcpp, STAAR, MultiSTAAR, SCANG, dplyr, SeqArray, TxDb.Hsapiens.UCSC.hg38.knownGene, GMMAT, Matrix, methods)
importFrom("stats", "pchisq", "lm", "model.matrix", "quantile", "rnorm", "binomial")
importFrom("SeqVarTools", "isSNV")
importFrom("GenomicFeatures", "genes", "promoters")
importFrom("GENESIS", "makeSparseMatrix")

useDynLib(STAARpipeline, .registration = TRUE)

# functions
export(fit_nullmodel,
       genesis2staar_nullmodel,
       staar2scang_nullmodel,
       Individual_Analysis,Individual_Analysis_cond,Individual_Analysis_cond_spa,
       Gene_Centric_Coding,Gene_Centric_Coding_cond,Gene_Centric_Coding_cond_spa,
       Gene_Centric_Noncoding,Gene_Centric_Noncoding_cond,Gene_Centric_Noncoding_cond_spa,
       ncRNA,ncRNA_cond,ncRNA_cond_spa,
       Sliding_Window,Sliding_Window_cond,Sliding_Window_cond_spa,
       Dynamic_Window_SCANG,
       LD_pruning)