topMotif: TOP Motif detection

In JokingHero/ORFik: Open Reading Frames in Genomics

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)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.