biobroom v1.4.2

by John D Storey

Turn Bioconductor objects into tidy data frames

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

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biobroom: Tidying up computational biology

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy/augment/glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

biobroom implements tidying methods for both S3 and S4 classes. Objects that can be tidied include

  • ExpressionSet objects
  • RangedSummarizedExperiment objects
  • MSnSet objects
  • per-gene differential expression tests from limma, edgeR, and DESeq2
  • qvalue multiple hypothesis testing objects

Installation

The package can be installed with (requires devtools):

devtools::install_github("StoreyLab/biobroom")

Find out more about the provided methods with:

library(biobroom)
?edgeR_tidiers
?DESeq2_tidiers
?limma_tidiers
?ExpressionSet_tidiers
?MSnSet_tidiers
?GRangesList
?GRanges
?SummarizedExperiment_tidiers

Note on returned values

All biobroom tidy and augment methods, since they tend to be large data frames, return a tbl_df by default (this prevents them from printing many rows at once, while still acting like a traditional data.frame). To change this to a data.frame or data.table, you can set the biobroom.return option:

options(biobroom.return = "data.frame")
options(biobroom.return = "data.table")

Functions in biobroom

Name Description
SummarizedExperiment_tidiers Tidying methods for Biobase's SummarizedExperiment objects
list_tidiers Tidiers for return values from functions that aren't S3 objects
DESeq2_tidiers Tidying methods for DESeq2 DESeqDataSet objects
tidy.GRanges Tidying methods for GRanges and GRangesList objects.
biobroom Convert Bioconductor Object into Tidy Data Frames
hammer ExpressionSet results from Hammer et al 2010
MSnSet_tidiers Tidying methods for Biobase's ExpressionSet objects
augment_sva Tidying methods for a sva list
qvalue_tidiers Tidying methods for a qvalue object
edgeR_tidiers Tidiers for edgeR's differential expression objects
tidy.deSet Tidying methods for edge's deSet object
limma_tidiers Tidiers for the output of limma (linear models for microarray analysis)
ExpressionSet_tidiers Tidying methods for Biobase's ExpressionSet objects
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Details

biocViews MultipleComparison, DifferentialExpression, Regression, GeneExpression, Proteomics, DataImport
License LGPL
LazyData true
VignetteBuilder knitr
URL https://github.com/StoreyLab/biobroom
BugReports https://github.com/StoreyLab/biobroom/issues
RoxygenNote 5.0.1

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