sample_annotation {SWATH2stats} | R Documentation

## 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.

### Details

Given dataframes of TRIC processed data and sample annotations, mash them together into something appropriate for downstream analyses.

This performs some quick sanity checks on the data and annotations and creates the 'Condition', 'BioReplicate', and 'Run' columns along with other columns expected by MSstats/OpenSWATH.

### Value

Returns a dataframe with each row annotated for the study design

### Author(s)

Peter Blattman

### Examples

     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- SWATH2stats::sample_annotation(OpenSWATH_data, Study_design, verbose=TRUE)
     summary(data)

[Package SWATH2stats version 1.20.1 Index]