kozakHeatmap {ORFik} | R Documentation

## 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)

[Package ORFik version 1.8.6 Index]