R/globals.R

In vivaldi: Viral Variant Location and Diversity

globalVariables(unique(c(
  # af_distribution:
  "minorfreq",
  # arrange_data:
  "ALT", "ALT_COUNT", "ALT_FREQ", "ALT_TYPE", "ANN", "CHROM", "gt_AD", "major", "majorcount", "majorfreq", "minor", "minorcount", "minorfreq", "POS", "REF", "REF_COUNT", "REF_FREQ",
  # dNdS_segment:
  "annotation", "dNdS", "feature_id", "n.x", "n.y", "SPLICEFORMS",
  # filter_variants:
  "ALT_FREQ", "ALT_FREQ.x", "ALT_FREQ.y", "gt_DP", "gt_DP.x", "gt_DP.y",
  # plot_shannon:
  "CHROM", "genome_shannon_perkb", "POS", "shannon_chrom_perkb", "shannon_ntpos",
  # position_allele_freq:
  "CHROM", "major", "majorfreq", "minor", "minorfreq", "POS",
  # prepare_annotations:
  "ANN",
  # read_reference_fasta_dna:
  "CHROM", "CHROM_SIZE", "V1",
  # shannon_entropy:
  "CHROM", "chrom_shannon", "SegmentSize", "shannon_ntpos",
  # shared_snv_plot:
  "CHROM", "count", "DF_filt", "POS", "totalsamp", "variant",
  # shared_snv_table:
  "ALT", "annotation", "CHROM", "count", "feature_id", "feature_type", "HGVS.p", "major", "majorfreq", "minor", "minorfreq", "POS", "protein_position", "REF", "totalsamp", "variant",
  # snv_genome:
  "annotation", "n",
  # snv_location:
  "ALT_TYPE", "major", "majorfreq", "minor", "minorfreq", "POS",
  # snv_segment:
  "annotation", "CHROM", "n",
  # tstv_plot:
  ".", "chrom_or_genome", "tstv_ratio_perkb",
  # tstv_ratio:
  "tstv", "tstv_chrom_count"
)))