test_binding: Statistical test for position-wise enrichment in selective...

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

Description

Using the background model estimated by fit_background_model, performs significance testing for enrichment of reads in sample1 compared to sample2 for all genes and positions.

Usage

test_binding(data, window_size, bpparam = BiocParallel::bpparam())

Arguments

data	A serp_data object. fit_background_model must have been run on the data.
window_size	Neighborhood size for the confidence interval calculation in nucleotides. If missing, the default window size of the data set will be used.
bpparam	A BiocParallelParam-class object.

Details

Enrichment spikes at individual positions are likely not indicative of real chaperone binding. Nevertheless, they frequently occur, probably due to ligation and/or sequencing bias. To alleviate this problem somewhat, read counts within a window_size-wide neighborhood are summed up individually for sample1 and sample2 and used for significance testing. This results in strongly correlatd p-values, therefore the Benjamini-Yekutieli-procedure is used for FDR control. sample1 and sample2 from fit_background_model are used. Note that the binning mode (bynuc or byaa) previously given to fit_background_model will be used.

Value

A serp_data object.

See Also

get_binding_pvalues, fit_background_model, get_binding_positions, plot_binding_positions

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