score_transcripts_single_motif {transite} | R Documentation

## Scores transadsadscripts with position weight matrices

### Description

This function is used to count the putative binding sites (i.e., motifs) in a set of sequences for the specified RNA-binding protein sequence motifs and returns the result in a data frame, which is aggregated by `score_transcripts` and subsequently used by `calculate_motif_enrichment` to obtain binding site enrichment scores.

### Usage

    score_transcripts_single_motif(
      motif,
      sequences,
      max_hits = 5,
      threshold_method = c("p_value", "relative"),
      threshold_value = 0.25^6,
      cache_path = paste0(tempdir(), "/sc/")
    )

### Arguments

`motif` | a Transite motif that is used to score the specified sequences
`sequences` | character vector of named sequences (only containing upper case characters A, C, G, T), where the names are RefSeq identifiers and sequence type qualifiers (`"3UTR"`, `"5UTR"`, `"mRNA"`), e.g. `"NM_010356|3UTR"`
`max_hits` | maximum number of putative binding sites per mRNA that are counted
`threshold_method` | either `"p_value"` (default) or `"relative"`. If `threshold_method` equals `"p_value"`, the default `threshold_value` is `0.25^6`, which is lowest p-value that can be achieved by hexamer motifs, the shortest supported motifs. If `threshold_method` equals `"relative"`, the default `threshold_value` is `0.9`, which is 90% of the maximum PWM score.
`threshold_value` | semantics of the `threshold_value` depend on `threshold_method` (default is 0.25^6)
`cache_path` | the path to a directory where scores are cached. The scores of each motif are stored in a separate file that contains a hash table with RefSeq identifiers and sequence type qualifiers as keys and the number of binding sites as values. If is.null(cache_path), scores will not be cached.

### Value

A list with the following items:

`motif_id` | the motif identifier of the specified motif
`motif_rbps` | the gene symbol of the RNA-binding protein(s)
`absolute_hits` | the absolute frequency of binding sites per motif in all transcripts
`relative_hits` | the relative, i.e., absolute divided by total, frequency of binding sites per motif in all transcripts
`total_sites` | the total number of potential binding sites
`one_hit`, `two_hits`, ... | number of transcripts with one, two, three, ... binding sites

### See Also

Other matrix functions: `calculate_motif_enrichment()`, `run_matrix_spma()`, `run_matrix_tsma()`, `score_transcripts()`

[Package transite version 1.6.2 Index]