TOP.Motif.ecdf {ORFik} | R Documentation

## TOP Motif ecdf plot

### Description

Given sequences, DNA or RNA. And some score, scanning efficiency (SE), ribo-seq fpkm, TE etc.

### Usage

    TOP.Motif.ecdf(
      seqs,
      rate,
      start = 1,
      stop = max(nchar(seqs)),
      xlim = c("q10", "q99"),
      type = "Scanning efficiency",
      legend.position.1st = c(0.75, 0.28),
      legend.position.motif = c(0.75, 0.28)
    )

### Arguments

`seqs` | the sequences (character vector, DNAStringSet), of 5' UTRs (leaders). See example below for input.
`rate` | a scoring vector (equal size to seqs)
`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
`xlim` | What interval of rate values you want to show type: numeric or quantile of length 2, 1. default c("q10","q99"). bigger than 10 percentile and less than 99 percentile. 2. Set to numeric values, like c(5, 1000), 3. Set to NULL if you want all values. Backend uses coord_cartesian.
`type` | What type is the rate scoring ? default ("Scanning efficiency")
`legend.position.1st` | adjust left plot label position, default c(0.75, 0.28), ("none", "left", "right", "bottom", "top", or two-element numeric vector)
`legend.position.motif` | adjust right plot label position, default c(0.75, 0.28), ("none", "left", "right", "bottom", "top", or two-element numeric vector)

### Details

Top motif defined as a TSS of C and 4 T's or C's (pyrimidins) downstream of TSS C.

The right plot groups: C nucleotide, TOP motif (C, then 4 pyrimidines) and OTHER (all other TSS variants).

### Value

a ggplot gtable of the TOP motifs in 2 plots

### 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)
      # Some toy ribo-seq fpkm scores on cds
      set.seed(3)
      fpkm <- sample(1:115, length(leadersCage), replace = TRUE)
      # Standard arguments
      TOP.Motif.ecdf(seqs, fpkm, type = "ribo-seq FPKM",
                     legend.position.1st = "bottom",
                     legend.position.motif = "bottom")
      # with no zoom on x-axis:
      TOP.Motif.ecdf(seqs, fpkm, xlim = NULL,
                     legend.position.1st = "bottom",
                     legend.position.motif = "bottom")
    }

    ## End(Not run)

[Package ORFik version 1.10.13 Index]