get_binding_positions_by_threshold: Extract binding regions based on a threshold

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

Description

Calculates binding regions given a threshold. For each gene, enrichment confidence intervals over smoothed read counts are calculated by binom_ci_profile. If the lower confidence bound is above the threshold at a position, this position is considered bound with high confidence. If the threshold lies within the confidence interval for a position, this position is considered bound with low confidence. Positions with the upper bound of the confidence interval below the threshold are considered unbound.

Usage

get_binding_positions_by_threshold(
  data,
  sample1,
  sample2,
  bin,
  window_size,
  skip_5prime = 0,
  skip_3prime = 0,
  conf.level = 0.95,
  bpparam = BiocParallel::bpparam(),
  threshold = 1
)

Arguments

data	A serp_data object.
sample1	Name of the first sample (the numerator). If missing, the default sample1 of the data set will be used.
sample2	Name of the second sample (the denominator). If missing, the default sample2 of the data set will be used.
bin	Binning mode (bynuc or byaa). If missing, the default binning level of the data set will be used.
window_size	Neighborhood size for the confidence interval calculation in nucleotides. If missing, the default window size of the data set will be used.
skip_5prime	How many nucleotides to skip at the 5' end of the ORF. Useful if you know that the 5' end contains artifacts.
skip_3prime	How many nucleotides to skip at the 3' end of the ORF. useful if you know that the 3' end contains artifacts.
conf.level	Confidence level.
bpparam	A BiocParallelParam-class object.
threshold	The enrichment threshold.

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 sample1.

sample2

Sum of counts of sample2 within the binding region. Note that the actual column name is the value of sample1.

binding_class

Binding class of the binding region. 2 for high-confidence regions, 1 for low-confidence regions.

See Also

get_binding_positions, plot_binding_positions

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