The PhIPData
class is used to store experimental results from
phage-immunoprecipitation sequencing (PhIP-set) experiments in a
matrix-like container.
Building on the
RangedSummarizedExperiment
class, PhIPData
contains all of functionality of
SummarizedExperiments
and includes additional operations to facilitate
analysis with PhIP-seq data. Like SummarizedExperiments
, a key feature
of PhIPData
is the coordination of metadata when subsetting PhIPData
objects. For example, if you wanted to examine experimental data for
peptides from one particular virus, you can subset the experimental data
and the associated peptide annotation with one command. This ensures all
metadata (for samples, peptides, etc.) remain synced with the
experimental data throughout analysis.
We recommend installing the stable release version of PhIPData
in
Bioconductor. This can be done using BiocManager
:
if (!require("BiocManager"))
install.packages("BiocManager")
BiocManager::install("PhIPData")
To load the package:
library(PhIPData)
As reflected in the figure below, the structure of a PhIPData
object
is nearly identical to the structure of a
SummarizedExperiment
/RangedSummarizedExperiment
object.
Each object contains at least three assays of data. These assays are:
counts
: matrix of raw read counts,logfc
: matrix of log10 estimated fold-changes (in comparison to
negative control samples),prob
: matrix of probabilities (p-values or posterior
probabilities) associated with whether a sample shows an enriched
antibody response to the particular peptide.The rows of a PhIPData
object represent peptides of interest and the
columns represent samples. Sample and peptide metadata are stored in
DataFrame
s. Each row of the metadata DataFrame
specifies the
peptide/sample, and the columns represent different features associated
with the peptides/samples.
In addition to sample- and peptide-specific metadata, experimental
metadata such as associated papers, experimental parameters, sequencing
dates, etc. are stored in a list-like component named metadata
.
Schematic of a PhIPData object. Commands used to access each component of the object are listed underneath its visual representation. Code in black indicates functions specific to `PhIPData` objects while functions in red extend `SummarizedExperiment` functions. Here, `pd` is a generic `PhIPData` object.
For an example of how to use PhIPData
objects, please see the package
vignette.
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