get_binding_positions: Extract statistically significant binding regions

In ilia-kats/RiboSeqTools: Tools for analysis of selective ribosome profiling (SeRP) data

Description

Calculates continuous binding regions at given FDR.

Usage

get_binding_positions(data, fdr = 0.01)

Arguments

data	A serp_data object. test_binding must have been run on the data.
fdr	False discovery rate.

Value

A tibble with the following columns:

exp

Experiment.

rep

Replicate.

gene

Gene.

start

Start of continuous binding region. If the binning mode for fit_background_model was byaa, this will be in codons, otherwise in nucleotides.

end

End of continuous binding region.

width

Width of continuous binding region.

sample1

Sum of counts of sample1 within the binding region. Note that the actual column name is the value of sample1given to fit_background_model.

sample2

Sum of counts of sample2 within the binding region. Note that the actual column name is the value of sample1given to fit_background_model.

See Also

fit_background_model, test_binding, plot_binding_positions, get_binding_positions_by_threshold

ilia-kats/RiboSeqTools documentation built on Oct. 5, 2020, 7:41 p.m.