NAMESPACE

exportPattern("^[[:alpha:]]+")
import(Rcpp, STAAR, MetaSTAAR, STAARpipeline, dplyr, SeqArray, TxDb.Hsapiens.UCSC.hg38.knownGene, Matrix, methods)
import(STAARpipelineSummary, except = genes)
importFrom("stats", "pchisq", "lm", "model.matrix", "quantile", "rnorm", "binomial")
importFrom("SeqVarTools", "isSNV")
importFrom("GenomicFeatures", "genes", "promoters")
importFrom("expm", "sqrtm")
importFrom("MASS", "ginv")
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "abline", "legend", "par", "plot")
importFrom("utils", "write.csv")


# functions
export(individual_analysis_MetaSTAARlite_worker,
       individual_analysis_MetaSTAARlite,
       individual_analysis_MetaSTAARlite_cond,
       coding_MetaSTAARlite_worker,
       coding_MetaSTAARlite,
       coding_MetaSTAARlite_cond,
       custom_MetaSTAARlite_worker,
       custom_MetaSTAARlite,
       custom_MetaSTAARlite_cond,
       noncoding_MetaSTAARlite_worker,
       noncoding_MetaSTAARlite,
       noncoding_MetaSTAARlite_cond,
       ncRNA_MetaSTAARlite_worker,
       ncRNA_MetaSTAARlite,
       ncRNA_MetaSTAARlite_cond,
       MetaSTAARlite_worker_sumstat,
       MetaSTAARlite_worker_cov,
       MetaSTAARlite_worker_cov_cond,
       MetaSTAARlite_merge,
       MetaSTAARlite_merge_cond,
       Gene_Centric_Coding_Results_Summary_meta,
       Gene_Centric_Noncoding_Results_Summary_meta,
       Individual_Analysis_Results_Summary_meta)