sample_annotation {SWATH2stats} | R Documentation

## sample_annotation: Annotate the SWATH data with the sample information

### Description

For statistical analysis and filtering the measurements need to be annotated with Filename, Condition, BioReplicate, and Run. This functions takes this information from a txt file containing this meta-data.

### Usage

    sample_annotation(data, sample.annotation, data.type="OpenSWATH",
    column.file = "filename", change.run.id = TRUE, verbose=FALSE)

### Arguments

`data` | A data frame containing SWATH data.
`sample.annotation` | A data frame containing the columns: Filename, Condition, BioReplicate, Run. The values contained in the column filename have to be present in the filename of the SWATH data.
`data.type` | Option to specify the format of the table, if the column names from an OpenSWATH output or MSstats table are used.
`column.file` | Option to specify the column name where the injection file is specified. Default is set to "filename".
`change.run.id` | Option to choose if the run\_id column shall be reassigned to a unique value combining the values of Condition, BioReplicate and Run. (Option only possible if data is of format "OpenSWATH")
`verbose` | Option to turn on reporting on which filename it is working on.

### Value

Returns a dataframe with each row annotated for the study design

### Author(s)

Peter Blattmann

### Examples

    data("OpenSWATH_data", package="SWATH2stats")
    data("Study_design", package="SWATH2stats")
    data <- sample_annotation(OpenSWATH_data, Study_design)

[Package SWATH2stats version 1.17.5 Index]