SWATH2stats (version 1.2.3)

count_analytes: 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.

Examples

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