topMotif {ORFik} | R Documentation

## TOP Motif detection

### Description

Per leader, detect if the leader has a TOP motif at TSS (5' end of leader) TOP motif defined as: (C, then 4 pyrimidines)

### Usage

    topMotif(seqs, start = 1, stop = max(nchar(seqs)), return.sequence = TRUE)

### Arguments

`seqs` | the sequences (character vector, DNAStringSet), of 5' UTRs (leaders) start region. seqs must be of minimum widths start - stop + 1 to be included. See example below for input.
`start` | position in seqs to start at (first is 1), default 1.
`stop` | position in seqs to stop at (first is 1), default max(nchar(seqs)), that is the longest sequence length
`return.sequence` | logical, default TRUE, return as data.table with sequence as columns in addition to TOP class. If FALSE, return character vector.

### Value

default: return.sequence == FALSE, a character vector of either TOP, C or OTHER. C means leaders started on C, Other means not TOP and did not start on C. If return.sequence == TRUE, a data.table is returned with the base per position in the motif is included as additional columns (per position called seq1, seq2 etc) and a id column called X.gene_id (with names of seqs).

### Examples

    ## Not run:
    if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19")) {
      txdbFile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                              package = "GenomicFeatures")
      #Extract sequences of Coding sequences.
      leaders <- loadRegion(txdbFile, "leaders")

      # Should update by CAGE if not already done
      cageData <- system.file("extdata", "cage-seq-heart.bed.bgz",
                              package = "ORFik")
      leadersCage <- reassignTSSbyCage(leaders, cageData)
      # Get region to check
      seqs <- startRegionString(leadersCage, NULL,
            BSgenome.Hsapiens.UCSC.hg19::Hsapiens, 0, 4)
      topMotif(seqs)
      }

    ## End(Not run)

[Package ORFik version 1.8.6 Index]