readQFeatures {QFeatures} | R Documentation

## QFeatures from tabular data

### Description

Convert tabular data from a spreadsheet or a `data.frame` into a `QFeatures` object.

### Usage

    readQFeatures(table, ecol, fnames, ..., name = NULL)

    readSummarizedExperiment(table, ecol, fnames, ...)

### Arguments

`table` | 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.
`ecol` | A `numeric` indicating the indices of the columns to be used as expression values. Can also be a `character` indicating the names of the columns. Caution must be taken if the column names are composed of special characters like `(` or `-` that will be converted to a `.` by the `read.csv` function. If `ecol` does not match, the error message will display the column names as seen by the `read.csv` function.
`fnames` | An optional `character(1)` or `numeric(1)` indicating the column to be used as feature names.
`...` | Further arguments that can be passed on to `read.csv` except `stringsAsFactors`, which is always `FALSE`.
`name` | An `character(1)` to name assay in the `QFeatures` object. If not set, `features` is used.

### Value

An instance of class QFeatures or SummarizedExperiment.

### Functions

- `readQFeatures`: See description.

- `readSummarizedExperiment`: Convert tabular data from a spreadsheet or a `data.frame` into a `SummarizedExperiment` object.

### Author(s)

Laurent Gatto

### See Also

The QFeatures class for an example on how to use `readQFeatures` and how to further manipulate the resulting data.

### Examples

    ## Load a data.frame with PSM-level data
    data(hlpsms)

    ## Create the QFeatures object
    fts2 <- readQFeatures(hlpsms, ecol = 1:10, name = "psms")
    fts2

[Package QFeatures version 1.0.0 Index]