TOP.Motif.ecdf: TOP Motif ecdf plot

In JokingHero/ORFik: Open Reading Frames in Genomics

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)

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