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| Author:       | Florent Chuffart                                  |

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+---------------+---------------------------------------------------+

| License:      | CeCILL                                            |

+---------------+---------------------------------------------------+

Package: nucleominer

Maintainer: Florent Chuffart <florent.chuffart@ens-lyon.fr>

Author: Florent Chuffart

License: CeCILL 

Title: nm

Depends: seqinr, plotrix, DESeq, cachecache

common_nuc_results, ##<< Common wp nuc maps

config=NULL ##<< GLOBAL config variable

) {

  tmp_combi_key = paste(combi[1], combi[2], sep="_")

  tmp_common_nucs = common_nuc_results[[tmp_combi_key]]

  tmp_common_nucs = tmp_common_nucs[tmp_common_nucs$roi_index == roi_index, ]

  tmp_fuzzy = fuzzy_maps[[combi[1]]]

  tmp_fuzzy = tmp_fuzzy[tmp_fuzzy$roi_index == roi_index, ]

  tmp_wp = wp_maps[[combi[1]]]

  if (length(tmp_unr_nucs_1[,1]) == 0) {return(NULL)}

  agg_unr_1 = tmp_unr_nucs_1

  tmp_fuzzy = fuzzy_maps[[combi[2]]]

  tmp_fuzzy = tmp_fuzzy[tmp_fuzzy$roi_index == roi_index, ]

  tmp_wp = wp_maps[[combi[2]]]

  tr_agg_unr_2 = translate_regions(agg_unr_2, combi, roi_index, roi=roi, config=config)

  tr_agg_unr_2 = union_regions(tr_agg_unr_2)

  all_unr = union_regions(rbind(agg_unr_1, tr_agg_unr_2))

  tmp_wp = wp_maps[[combi[1]]]

  tmp_wp = tmp_wp[tmp_wp$wp==1,]

  tmp_wp = tmp_wp[tmp_wp$roi_index == roi_index, ]

  }))

  wp_nucs_1 = tmp_wp[tmp_wp$index_nuc %in% tmp_index, ]

  tmp_wp = wp_maps[[combi[2]]]

  tmp_wp = tmp_wp[tmp_wp$wp==1,]

  tmp_wp = tmp_wp[tmp_wp$roi_index == roi_index, ]

    tr_wp_nucs_2 = translate_regions(wp_nucs_2, combi, roi_index, roi=roi, config=config)      

  }

  all_wp = union_regions(rbind(wp_nucs_1[,1:4], tr_wp_nucs_2))

  non_inter_unr = substract_region(all_unr, all_wp)

  non_inter_unr = crop_fuzzy(non_inter_unr, roi, combi[1], config)

  if (is.null(non_inter_unr)) { return(NULL) }