count_analytes: Counts the analytes across the different injections

In peterblattmann/SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

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)
 }

peterblattmann/SWATH2stats documentation built on July 2, 2023, 9:42 p.m.