findPeaksPerGene {ORFik} | R Documentation

## Find peaks per gene

### Description

For finding the peaks (stall sites) per gene, with some default filters. A peak is basically a position of very high coverage compared to its surrounding area, as measured using zscore.

### Usage

    findPeaksPerGene(
      tx,
      reads,
      top_tx = 0.5,
      min_reads_per_tx = 20,
      min_reads_per_peak = 10,
      type = "max"
    )

### Arguments

`tx` | a GRangesList
`reads` | a GAlignments or GRanges, must be 1 width reads like p-shifts, or other reads that is single positioned. It will work with non 1 width bases, but you then get larger areas for peaks.
`top_tx` | numeric, default 0.50 (only use 50% top transcripts by read counts).
`min_reads_per_tx` | numeric, default 20. Gene must have at least 20 reads, applied before type filter.
`min_reads_per_peak` | numeric, default 10. Peak must have at least 10 reads.
`type` | character, default "max". Get only max peak per gene. Alternatives: "all", all peaks passing the input filter will be returned. "median", only peaks that is higher than the median of all peaks. "maxmedian": get first "max", then median of those.

### Details

For more details see reference, which uses a slightly different method by zscore of a sliding window instead of over the whole tx.

### Value

a data.table of gene_id, position, counts of the peak, zscore and standard deviation of the peak compared to rest of gene area.

### References

doi: 10.1261/rna.065235.117

### Examples

    df <- ORFik.template.experiment()
    cds <- loadRegion(df, "cds")
    # Load ribo seq from ORFik
    rfp <- fimport(df[3,]$filepath)
    # All transcripts passing filter
    findPeaksPerGene(cds, rfp, top_tx = 0)
    # Top 50% of genes
    findPeaksPerGene(cds, rfp)

[Package ORFik version 1.12.13 Index]