count_analytes: Counts the analytes across the different injections

Description Usage Arguments Value Author(s) Examples

View source: R/count_analytes.R

Description

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

Usage

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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

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

peterblattmann/SWATH2stats documentation built on April 20, 2021, 12:02 p.m.