count_analytes: Counts the analytes across the different injections
In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

Description Usage Arguments Value Author(s) Examples

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

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

`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.

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

Peter Blattmann

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