R/RcppExports.R

In scPipe: pipeline for single cell RNA-seq data analysis

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

rcpp_sc_trim_barcode_paired <- function(outfq, r1, r2, bs1, bl1, bs2, bl2, us, ul, rmlow, rmN, minq, numbq, write_gz) {
    invisible(.Call(`_scPipe_rcpp_sc_trim_barcode_paired`, outfq, r1, r2, bs1, bl1, bs2, bl2, us, ul, rmlow, rmN, minq, numbq, write_gz))
}

rcpp_sc_exon_mapping <- function(inbam, outbam, annofn, am, ge, bc, mb, bc_len, bc_vector, UMI_len, stnd, fix_chr, nthreads) {
    invisible(.Call(`_scPipe_rcpp_sc_exon_mapping`, inbam, outbam, annofn, am, ge, bc, mb, bc_len, bc_vector, UMI_len, stnd, fix_chr, nthreads))
}

rcpp_sc_exon_mapping_df_anno <- function(inbam, outbam, anno, am, ge, bc, mb, bc_len, bc_vector, UMI_len, stnd, fix_chr, nthreads) {
    invisible(.Call(`_scPipe_rcpp_sc_exon_mapping_df_anno`, inbam, outbam, anno, am, ge, bc, mb, bc_len, bc_vector, UMI_len, stnd, fix_chr, nthreads))
}

rcpp_sc_demultiplex <- function(inbam, outdir, bc_anno, max_mis, am, ge, bc, mb, mito, has_UMI, nthreads) {
    invisible(.Call(`_scPipe_rcpp_sc_demultiplex`, inbam, outdir, bc_anno, max_mis, am, ge, bc, mb, mito, has_UMI, nthreads))
}

rcpp_sc_clean_bam <- function(inbam, outbam, bc_anno, max_mis, am, ge, bc, mb, mito, nthreads) {
    invisible(.Call(`_scPipe_rcpp_sc_clean_bam`, inbam, outbam, bc_anno, max_mis, am, ge, bc, mb, mito, nthreads))
}

rcpp_sc_gene_counting <- function(outdir, bc_anno, UMI_cor, gene_fl) {
    invisible(.Call(`_scPipe_rcpp_sc_gene_counting`, outdir, bc_anno, UMI_cor, gene_fl))
}

rcpp_sc_detect_bc <- function(infq, outcsv, prefix, bc_len, max_reads, number_of_cells, min_count, max_mismatch, white_list) {
    invisible(.Call(`_scPipe_rcpp_sc_detect_bc`, infq, outcsv, prefix, bc_len, max_reads, number_of_cells, min_count, max_mismatch, white_list))
}