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      "topics": [
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      "title": "Motif Enrichment calculation",
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      "title": "Check Validity of Set of _k_-mers",
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      "title": "_k_-mer Enrichment between Foreground and Background Sets",
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      "title": "Correction for Homopolymeric Stretches",
      "concept": [
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      "title": "Creates Transite motif object from character vector of _k_-mers",
      "topics": [
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      "title": "_k_-mer Enrichment Volcano Plot",
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      "page": "generate_permuted_enrichments",
      "title": "Generate Random Permutations of the Enrichment Data",
      "concept": [
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "generate_permuted_enrichments"
      ]
    },
    {
      "page": "geometric_mean",
      "title": "Geometric Mean",
      "topics": [
        "geometric_mean"
      ]
    },
    {
      "page": "get_motif_by_id",
      "title": "Retrieve motif objects by id",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motif_by_id"
      ]
    },
    {
      "page": "get_motif_by_rbp",
      "title": "Retrieve motif objects by gene symbol",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motif_by_rbp"
      ]
    },
    {
      "page": "get_motifs",
      "title": "Retrieve list of all motifs",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motifs"
      ]
    },
    {
      "page": "get_motifs_meta_info",
      "title": "Displays motif meta information.",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_motifs_meta_info"
      ]
    },
    {
      "page": "get_ppm",
      "title": "Get Position Probability Matrix (PPM) from motif object",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "get_ppm"
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    },
    {
      "page": "init_iupac_lookup_table",
      "title": "Initializes the IUPAC lookup table",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "init_iupac_lookup_table"
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    },
    {
      "page": "kmers_enrichment",
      "title": "Example _k_-mer Enrichment Data",
      "topics": [
        "kmers_enrichment"
      ]
    },
    {
      "page": "motifs",
      "title": "Transite Motif Database",
      "topics": [
        "motifs"
      ]
    },
    {
      "page": "p_combine",
      "title": "P-value aggregation",
      "topics": [
        "p_combine"
      ]
    },
    {
      "page": "RBPMotif-class",
      "title": "An S4 class to represent a RBPMotif",
      "topics": [
        ".RBPMotif",
        "get_heptamers",
        "get_heptamers,RBPMotif-method",
        "get_hexamers",
        "get_hexamers,RBPMotif-method",
        "get_id",
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        "get_iupac",
        "get_iupac,RBPMotif-method",
        "get_motif_matrix",
        "get_motif_matrix,RBPMotif-method",
        "get_rbps",
        "get_rbps,RBPMotif-method",
        "get_source",
        "get_source,RBPMotif-method",
        "get_species",
        "get_species,RBPMotif-method",
        "get_type",
        "get_type,RBPMotif-method",
        "get_width",
        "get_width,RBPMotif-method",
        "RBPMotif-class",
        "show,RBPMotif-method"
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    },
    {
      "page": "run_kmer_spma",
      "title": "_k_-mer-based Spectrum Motif Analysis",
      "concept": [
        "SPMA functions",
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "run_kmer_spma"
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    },
    {
      "page": "run_kmer_tsma",
      "title": "_k_-mer-based Transcript Set Motif Analysis",
      "concept": [
        "TSMA functions",
        "list(\"k\")\n-mer functions"
      ],
      "topics": [
        "run_kmer_tsma"
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    },
    {
      "page": "run_matrix_spma",
      "title": "Matrix-based Spectrum Motif Analysis",
      "concept": [
        "SPMA functions",
        "matrix functions"
      ],
      "topics": [
        "run_matrix_spma"
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    },
    {
      "page": "run_matrix_tsma",
      "title": "Matrix-based Transcript Set Motif Analysis",
      "concept": [
        "TSMA functions",
        "matrix functions"
      ],
      "topics": [
        "run_matrix_tsma"
      ]
    },
    {
      "page": "score_sequences",
      "title": "Score Sequences with PWM",
      "topics": [
        "score_sequences"
      ]
    },
    {
      "page": "score_spectrum",
      "title": "Calculates spectrum scores and creates spectrum plots",
      "concept": [
        "SPMA functions"
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      "topics": [
        "score_spectrum"
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    {
      "page": "score_transcripts",
      "title": "Scores transcripts with position weight matrices",
      "concept": [
        "matrix functions"
      ],
      "topics": [
        "score_transcripts"
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    },
    {
      "page": "score_transcripts_single_motif",
      "title": "Scores transadsadscripts with position weight matrices",
      "concept": [
        "matrix functions"
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      "topics": [
        "score_transcripts_single_motif"
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    },
    {
      "page": "set_motifs",
      "title": "Set Transite motif database",
      "concept": [
        "motif functions"
      ],
      "topics": [
        "set_motifs"
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    },
    {
      "page": "SpectrumScore-class",
      "title": "An S4 class to represent a scored spectrum",
      "topics": [
        ".SpectrumScore",
        "get_adj_r_squared",
        "get_adj_r_squared,SpectrumScore-method",
        "get_consistency_score",
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        "get_consistency_score_n",
        "get_consistency_score_n,SpectrumScore-method",
        "get_consistency_score_p_value",
        "get_consistency_score_p_value,SpectrumScore-method",
        "get_model_degree",
        "get_model_degree,SpectrumScore-method",
        "get_model_f_statistic",
        "get_model_f_statistic,SpectrumScore-method",
        "get_model_f_statistic_p_value",
        "get_model_f_statistic_p_value,SpectrumScore-method",
        "get_model_residuals",
        "get_model_residuals,SpectrumScore-method",
        "get_model_slope",
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        "plot,SpectrumScore,ANY-method",
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        "SpectrumScore-class"
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    },
    {
      "page": "subdivide_data",
      "title": "Subdivides Sequences into _n_ Bins",
      "concept": [
        "SPMA functions"
      ],
      "topics": [
        "subdivide_data"
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    },
    {
      "page": "toy_motif_matrix",
      "title": "Toy Motif Matrix",
      "topics": [
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      "package": "libstdc++6",
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      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
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  "_vignettes": [
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      "source": "spma.Rmd",
      "filename": "spma.html",
      "title": "Spectrum Motif Analysis (SPMA)",
      "author": "Konstantin Krismer",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Analysis",
        "Results",
        "Additional information"
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      "created": "2018-09-18 21:57:58",
      "modified": "2020-08-25 15:05:46",
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