ribo_fft: Get periodogram data per read length

In JokingHero/ORFik: Open Reading Frames in Genomics

Get periodogram data per read length

Description

A data.table of periods and amplitudes, great to detect ribosomal read lengths. Uses 5' end of reads to detect periodicity. Works both before and after p-shifting. Plot results with ribo_fft_plot.

Usage

ribo_fft(footprints, cds, read_lengths = 26:34, firstN = 150)

Arguments

footprints	Ribosome footprints in either GAlignments or GRanges
cds	a GRangesList of coding sequences. Length must match length of argument mrna, and all must have length > arugment firstN.
read_lengths	integer vector, default: 26:34, which read length to check for. Will exclude all read_lengths that does not exist for footprints.
firstN	(integer) Represents how many bases of the transcripts downstream of start codons to use for initial estimation of the periodicity.

Value

a data.table with read_length, amplitude and periods

Examples

## Note, this sample data is not intended to be strongly periodic.
## Real data should have a cleaner peak for x = 3 (periodicity)
# Load sample data
df <- ORFik.template.experiment()
# Load annotation
loadRegions(df, "cds", names.keep = filterTranscripts(df))
# Select a riboseq library
df <- df[df$libtype == "RFP", ]
footprints <- fimport(filepath(df[1,], "default"))
fft_dt <-ribo_fft(footprints, cds)
ribo_fft_plot(fft_dt)

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