scoreTranscriptsSingleMotif {transite} | R Documentation |
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.
scoreTranscriptsSingleMotif(motif, sequences, max.hits = 5, threshold.method = "p.value", threshold.value = 0.25^6, cache.path = paste0(tempdir(), "/sc/"))
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 ( |
max.hits |
maximum number of putative binding sites per mRNA that are counted |
threshold.method |
either |
threshold.value |
semantics of the |
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. |
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 |
Other matrix functions: calculateMotifEnrichment
,
runMatrixSPMA
, runMatrixTSMA
,
scoreTranscripts