R: Read single-cell proteomics data as a QFeatures object from...

readSCP {scp}

R Documentation

Read single-cell proteomics data as a QFeatures object from tabular data and metadata

Description

Convert tabular quantitative MS data and metadata from a spreadsheet or a data.frame into a QFeatures object containing SingleCellExperiment objects.

Usage

readSCP(quantTable, metaTable, batchCol, channelCol, verbose = TRUE, ...)

Arguments

`quantTable`	File or object holding the quantitative data. Can be either a `character(1)` with the path to a text-based spreadsheet (comma-separated values by default, but see `...`) or an object that can be coerced to a `data.frame`. It is advised not to encode characters as factors.
`metaTable`	A `data.frame` or any object that can be coerced to a `data.frame`. `metaTable` is expected to contains all the sample meta information. Required fields are the acquisition batch (given by `batchCol`) and the acquisition channel within the batch (e.g. TMT channel, given by `channelCol`). Additional fields (e.g. sample type, acquisition date,...) are allowed and will be stored as sample meta data.
`batchCol`	A `numeric(1)` or `character(1)` pointing to the column of `quantTable` and `metaTable` that contain the batch names. Make sure that the column name in both table are either identical (if you supply a `character`) or have the same index (if you supply a `numeric`).
`channelCol`	A `numeric(1)` or `character(1)` pointing to the column of `metaTable` that contains the column names of the quantitive data in `quantTable` (see Example).
`verbose`	A `logical(1)` indicating whether the progress of the data reading and formatting should be printed to the console. Default is `TRUE`.
`...`	Further arguments that can be passed on to read.csv except `stringsAsFactors`, which is always `FALSE`.

Value

An instance of class QFeatures. The expression data of each batch is stored in a separate assay as a SingleCellExperiment object.

Note

The SingleCellExperiment class is built on top of the RangedSummarizedExperiment class. This means that some column names are forbidden in the rowData. Avoid using the following names: seqnames, ranges, strand, start, end, width, element

Author(s)

Laurent Gatto, Christophe Vanderaa

Examples


## Load an example table containing MaxQuant output
data("mqScpData")

## Load the (user-generated) annotation table
data("sampleAnnotation")

## Format the tables into a QFeatures object
readSCP(quantTable = mqScpData,
        metaTable = sampleAnnotation,
        batchCol = "Set",
        channelCol = "Channel")

[Package scp version 1.0.0 Index]