In UCLouvain-CBIO/scpdata: Single-Cell Proteomics Data Package

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html
)

The scpdata package

scpdata disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) data sets formatted using the scp data structure. The data structure is described in the scp vignette.

In this vignette, we describe how to access the SCP data sets. To start, we load the scpdata package.

library("scpdata")

Load data from ExperimentHub

The data is stored using the ExperimentHub infrastructure. We first create a connection with ExperimentHub.

eh <- ExperimentHub()

You can list all data sets available in scpdata using the query function.

query(eh, "scpdata")

Another way to get information about the available data sets is to call scpdata(). This will retrieve all the available metadata. For example, we can retrieve the data set titles along with the description to make an informed choice about which data set to choose.

info <- scpdata()
knitr::kable(info[, c("title", "description")])

To get one of the data sets (e.g. dou2019_lysates) you can either retrieve it using the ExperimentHub query function

scp <- eh[["EH3901"]]
scp

or you can the use the built-in functions from scpdata

scp <- dou2019_lysates()
scp

Data sets information

Each data set has been extensively documented in a separate man page (e.g. ?dou2019_lysates). You can find information about the data content, the acquisition protocol, the data collection procedure as well as the data sources and reference.

Data manipulation

For more information about manipulating the data sets, check the scp package. The scp vignette will guide you through a typical SCP data processing workflow. Once your data is loaded from scpdata you can skip section 2 Read in SCP data of the scp vignette.

Session information {-}

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "",
    crop = NULL
)

sessionInfo()

License

This vignette is distributed under a CC BY-SA license.

UCLouvain-CBIO/scpdata documentation built on Oct. 29, 2024, 4:22 p.m.