gettRNAscanSummary {tRNAscanImport}R Documentation

tRNAscanImport summary functions

Description

gettRNAscanSummary(): creates an DataFrame with aggregated information from the tRNAscan information.

gettRNAscanPlots(): If ggplot2 is installed a plot of the data is generated and returned.

plottRNAscan(): If ggplot2 is installed a plot of the data is generated and ploted directly.

Usage

gettRNAscanSummary(gr)

plottRNAscan(grl)

gettRNAscanPlots(grl)

## S4 method for signature 'GRanges'
gettRNAscanSummary(gr)

## S4 method for signature 'GRangesList'
plottRNAscan(grl)

## S4 method for signature 'GRangesList'
gettRNAscanPlots(grl)

Arguments

gr

a GRanges object created by import.tRNAscanAsGRanges or GRanges with equivalent information.

grl

a GRangesList object created with GRanges created by import.tRNAscanAsGRanges or GRanges with equivalent information.

Value

gettRNAscanSummary(): returns a DataFrame with the summarized results used for plotting internally.

gettRNAscanPlots(): returns a list of ggplots per column of data returned by gettRNAscanSummary().

plottRNAscan(): the function plots the output of gettRNAscanPlots directly to the current plotting device.

Examples

library(GenomicRanges, quietly = TRUE)
sce <- import.tRNAscanAsGRanges(system.file("extdata",
                               file = "sacCer3-tRNAs.ss.sort",
                               package = "tRNAscanImport"))
eco <- import.tRNAscanAsGRanges(system.file("extdata",
                        file = "eschColi_K_12_MG1655-tRNAs.ss.sort",
                        package = "tRNAscanImport"))
gettRNAscanSummary(sce)
plots <- gettRNAscanPlots(GRangesList(Sce = sce,
                                      Eco = eco))
[Package tRNAscanImport version 1.0.1 Index]