xtail-accessors: Results table of xtail results

In xryanglab/xtail: Genome-wide assessment of differential translations with ribosome profiling data

Results table of xtail results

Description

To retrieve the results from the xtail run use one of the accessor functions.

Usage

## S4 method for signature 'xtail'
conditions(object)

resultsNum(object, ...)

## S4 method for signature 'xtail'
resultsNum(object, ...)

resultsTable(object, ...)

## S4 method for signature 'xtail'
resultsTable(object, sort.by = NULL, log2FCs = FALSE, log2Rs = FALSE, ...)

summary(object, ...)

## S3 method for class 'xtail'
summary(object, alpha = 0.1, ...)

Arguments

object	a xtail object
...	optional arguments. Currently not used
sort.by	the column to sort with. Defaults to NULL to disable sorting.
log2FCs	TRUE or FALSE: Should log2 fold change values be returned? (defaults to TRUE)
log2Rs	TRUE or FALSE: Should log2 ratio values be returned? (defaults to TRUE)
alpha	cut off for summarizing results. Only results with a adjusted p-value lower than alpha will be reported.

Value

a DataFrame with the results or numeric vectors

Examples

data(xtailres)
resultsTable(xtailres)
conditions(xtailres)
resultsNum(xtailres)

# sorting or results
resultsTable(xtailres, sort.by = "pvalue.adjust")

xryanglab/xtail documentation built on April 13, 2022, 2:34 p.m.