R/RcppExports.R

In CreRecombinase/RColumbo: R Package to accompany the Columbo method

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

daal_cov <- function(X) {
    .Call('RColumbo_daal_cov', PACKAGE = 'RColumbo', X)
}

data_bytes <- function(h5file, groupname, dataname) {
    .Call('RColumbo_data_bytes', PACKAGE = 'RColumbo', h5file, groupname, dataname)
}

get_rownum_h5 <- function(h5file, groupname, dataname) {
    .Call('RColumbo_get_rownum_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname)
}

get_colnum_h5 <- function(h5file, groupname, dataname) {
    .Call('RColumbo_get_colnum_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname)
}

getGroups <- function(h5file) {
    .Call('RColumbo_getGroups', PACKAGE = 'RColumbo', h5file)
}

getObjects <- function(h5file, groupname) {
    .Call('RColumbo_getObjects', PACKAGE = 'RColumbo', h5file, groupname)
}

get_arraydim <- function(h5file, groupname, dataname) {
    .Call('RColumbo_get_arraydim', PACKAGE = 'RColumbo', h5file, groupname, dataname)
}

read_fmat_h5 <- function(hap_h5file, groupname, dataname, offset, chunksize) {
    .Call('RColumbo_read_fmat_h5', PACKAGE = 'RColumbo', hap_h5file, groupname, dataname, offset, chunksize)
}

read_dmat_h5 <- function(hap_h5file, groupname, dataname, offset, chunksize) {
    .Call('RColumbo_read_dmat_h5', PACKAGE = 'RColumbo', hap_h5file, groupname, dataname, offset, chunksize)
}

read_dmat_chunk_ind <- function(h5file, groupname, dataname, indvec) {
    .Call('RColumbo_read_dmat_chunk_ind', PACKAGE = 'RColumbo', h5file, groupname, dataname, indvec)
}

read_fmat_chunk_ind <- function(h5file, groupname, dataname, indvec) {
    .Call('RColumbo_read_fmat_chunk_ind', PACKAGE = 'RColumbo', h5file, groupname, dataname, indvec)
}

read_h5_df_col <- function(h5file, groupname, dataname, dclass, col_index) {
    .Call('RColumbo_read_h5_df_col', PACKAGE = 'RColumbo', h5file, groupname, dataname, dclass, col_index)
}

read_Rint_h5 <- function(h5file, groupname, dataname) {
    .Call('RColumbo_read_Rint_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname)
}

read_float_h5 <- function(h5file, groupname, dataname, offset, chunksize) {
    .Call('RColumbo_read_float_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, offset, chunksize)
}

read_double_h5 <- function(h5file, groupname, dataname, offset, chunksize) {
    .Call('RColumbo_read_double_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, offset, chunksize)
}

read_Rfloat_h5 <- function(h5file, groupname, dataname) {
    .Call('RColumbo_read_Rfloat_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname)
}

intersect_col <- function(h5file1, h5groupname1, h5colname1, h5file2, h5groupname2, h5colname2) {
    .Call('RColumbo_intersect_col', PACKAGE = 'RColumbo', h5file1, h5groupname1, h5colname1, h5file2, h5groupname2, h5colname2)
}

read_2dfmat_h5 <- function(h5file, groupname, dataname, row_offset, col_offset, row_chunksize, col_chunksize) {
    .Call('RColumbo_read_2dfmat_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, row_offset, col_offset, row_chunksize, col_chunksize)
}

read_2ddmat_h5 <- function(h5file, groupname, dataname, row_offset, col_offset, row_chunksize, col_chunksize) {
    .Call('RColumbo_read_2ddmat_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, row_offset, col_offset, row_chunksize, col_chunksize)
}

dmeansd_h5 <- function(h5file, groupname, dataname, dim = 0L) {
    .Call('RColumbo_dmeansd_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, dim)
}

write_dmatrix_h5 <- function(h5file, groupname, dataname, Nsnps, Nind, data, deflate_level) {
    .Call('RColumbo_write_dmatrix_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, Nsnps, Nind, data, deflate_level)
}

write_Rint_h5 <- function(h5file, groupname, dataname, data, deflate_level) {
    .Call('RColumbo_write_Rint_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, data, deflate_level)
}

write_Rnumeric_h5 <- function(h5file, groupname, dataname, data, deflate_level) {
    .Call('RColumbo_write_Rnumeric_h5', PACKAGE = 'RColumbo', h5file, groupname, dataname, data, deflate_level)
}

ip_cov <- function(Hpanela, Hpanelb, isDiag) {
    .Call('RColumbo_ip_cov', PACKAGE = 'RColumbo', Hpanela, Hpanelb, isDiag)
}

cov_2_cor <- function(covmat, rowvara, colvarb, isDiag) {
    invisible(.Call('RColumbo_cov_2_cor', PACKAGE = 'RColumbo', covmat, rowvara, colvarb, isDiag))
}

compute_shrinkage <- function(distmat, S, hmata, theta, m, Ne, cutoff, isDiag) {
    invisible(.Call('RColumbo_compute_shrinkage', PACKAGE = 'RColumbo', distmat, S, hmata, theta, m, Ne, cutoff, isDiag))
}

gen_sparsemat <- function(ldmat, istart, jstart, nSNPs) {
    .Call('RColumbo_gen_sparsemat', PACKAGE = 'RColumbo', ldmat, istart, jstart, nSNPs)
}

calcLD <- function(hmata, hmatb, mapa, mapb, m, Ne, cutoff, isDiag) {
    .Call('RColumbo_calcLD', PACKAGE = 'RColumbo', hmata, hmatb, mapa, mapb, m, Ne, cutoff, isDiag)
}

orthogonalize_covar <- function(Covariates) {
    .Call('RColumbo_orthogonalize_covar', PACKAGE = 'RColumbo', Covariates)
}

orthogonalize_data <- function(Data, covariates) {
    .Call('RColumbo_orthogonalize_data', PACKAGE = 'RColumbo', Data, covariates)
}

betaMatrix <- function(Genotype, Expression) {
    .Call('RColumbo_betaMatrix', PACKAGE = 'RColumbo', Genotype, Expression)
}

fastest_eQTL <- function(Genotype, Expression) {
    .Call('RColumbo_fastest_eQTL', PACKAGE = 'RColumbo', Genotype, Expression)
}

d_fastest_eQTL <- function(Genotype, Expression) {
    .Call('RColumbo_d_fastest_eQTL', PACKAGE = 'RColumbo', Genotype, Expression)
}

orthogonalize_dataset <- function(h5filename, newh5filename, covar_h5file, datagroup, datasetname, newdatasetname, chunksize, deflate_level) {
    invisible(.Call('RColumbo_orthogonalize_dataset', PACKAGE = 'RColumbo', h5filename, newh5filename, covar_h5file, datagroup, datasetname, newdatasetname, chunksize, deflate_level))
}