count_analytes {SWATH2stats} | R Documentation

## count_analytes: Counts analytes in 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 different 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)
    count_analytes(data)

[Package SWATH2stats version 1.17.5 Index]