count_analytes {SWATH2stats} | R Documentation

## Counts the analytes across the different injections

### Description

This functions counts the number of different peakgroups, peptides and proteins in different injections.

### Usage

    count_analytes(
      data,
      column_levels = c("transition_group_id", "FullPeptideName", "ProteinName"),
      column_by = "run_id",
      rm_decoy = TRUE
    )

### Arguments

`data` | A data frame containing SWATH data.
`column_levels` | Columns in which the number of unique identifiers should be counted.
`column_by` | Column for which the different identifiers should be counted for, e.g. for the different injections.
`rm_decoy` | Option to not remove decoy before counting.

### Value

Returns a data frame with the count of the different identifiers per e.g. injection.

### Author(s)

Peter Blattmann

### Examples

    {
     data("OpenSWATH_data", package="SWATH2stats")
     data("Study_design", package="SWATH2stats")
     data <- sample_annotation(OpenSWATH_data, Study_design)
     counts <- count_analytes(data)
     }

[Package SWATH2stats version 1.20.1 Index]