kozakHeatmap: Make sequence region heatmap relative to scoring

In JokingHero/ORFik: Open Reading Frames in Genomics

Make sequence region heatmap relative to scoring

Description

Given sequences, DNA or RNA. And some score, ribo-seq fpkm, TE etc. Create a heatmap divided per letter in seqs, by how strong the score is.

Usage

kozakHeatmap(
  seqs,
  rate,
  start = 1,
  stop = max(nchar(seqs)),
  center = ceiling((stop - start + 1)/2),
  min.observations = ">q1",
  skip.startCodon = FALSE,
  xlab = "TIS",
  type = "ribo-seq"
)

Arguments

seqs	the sequences (character vector, DNAStringSet)
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
center	position in seqs to center at (first is 1), center will be +1 in heatmap
min.observations	How many observations per position per letter to accept? numeric or quantile, default (">q1", bigger than quartile 1 (25 percentile)). You can do (10), to get all with more than 10 observations.
skip.startCodon	startCodon is defined as after centering (position 1, 2 and 3). Should they be skipped ? default (FALSE). Not relevant if you are not doing Translation initiation sites (TIS).
xlab	Region you are checking, default (TIS)
type	What type is the rate scoring ? default (ribo-seq)

Details

It will create blocks around the highest rate per position

Value

a ggplot of the heatmap

Examples

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

  # Get region to check
  kozakRegions <- startRegionString(cds, tx, BSgenome.Hsapiens.UCSC.hg19::Hsapiens
                                    , upstream = 4, 5)
  # Some toy ribo-seq fpkm scores on cds
  set.seed(3)
  fpkm <- sample(1:115, length(cds), replace = TRUE)
  kozakHeatmap(kozakRegions, fpkm, 1, 9, skip.startCodon = F)
}

## End(Not run)

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