defaults: Default parameters for a data set

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

Description

Named list of default values used in various functions. Usually, the default can be overriden by an argument to the respective function. Currently, the following defaults are recognized:

genename_column

Which column of the reference table to use for gene names.

bin

Bin level, one of byaa for codon-level binning or bynuc for nucleotide-level binning (corresponds to no binning).

sample1

Sample to use in the numerator of enrichment calculations.

sample2

Sample to use in the denominator of enrichment calculations.

window_size

Neighborhood size to use in enrichment CI calculations.

plot_ylim_enrichment

Y axis limit for enrichment plots.

plot_ybreaks_enrichment

Y axis breaks for enrichment plots.

plot_ylim_rpm

Y axis limit for RPM plots.

plot_ybreaks_rpm

Y axis breaks for RPM plots.

plot_fill_scale

A ggplot2 fill scale to use for enrichment plots. If this is a manual scale, value names must correspond to experiment names.

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