scoreTranscriptsSingleMotif {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 `scoreTranscripts` and subsequently used by `calculateMotifEnrichment` to obtain binding site enrichment scores.

### Usage

    scoreTranscriptsSingleMotif(motif, sequences, max.hits = 5,
      threshold.method = "p.value", 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: `calculateMotifEnrichment`, `runMatrixSPMA`, `runMatrixTSMA`, `scoreTranscripts`

[Package transite version 1.2.1 Index]