sample_annotation: Annotate the SWATH data with the sample information

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

Annotate the SWATH data with the sample information

Description

For statistical analysis and filtering the measurements need to be annotated with Filename, Condition, BioReplicate, and Run. This functions takes this information from a txt file containing this meta-data.

Usage

sample_annotation(
  data,
  sample_annotation,
  data_type = "OpenSWATH",
  column_file = "filename",
  change_run_id = TRUE,
  verbose = FALSE
)

Arguments

data	A data frame containing SWATH data.
sample_annotation	A data frame containing the columns: Filename, Condition, BioReplicate, Run. The values contained in the column filename have to be present in the filename of the SWATH data.
data_type	Option to specify the format of the table, if the column names from an OpenSWATH output or MSstats table are used.
column_file	Option to specify the column name where the injection file is specified. Default is set to "filename".
change_run_id	Option to choose if the run\_id column shall be reassigned to a unique value combining the values of Condition, BioReplicate and Run. (Option only possible if data is of format "OpenSWATH")
verbose	Option to turn on reporting on which filename it is working on.

Details

Given dataframes of TRIC processed data and sample annotations, mash them together into something appropriate for downstream analyses.

This performs some quick sanity checks on the data and annotations and creates the 'Condition', 'BioReplicate', and 'Run' columns along with other columns expected by MSstats/OpenSWATH.

Value

Returns a dataframe with each row annotated for the study design

Author(s)

Peter Blattman

Examples

 data("OpenSWATH_data", package="SWATH2stats")
 data("Study_design", package="SWATH2stats")
 data <- SWATH2stats::sample_annotation(OpenSWATH_data, Study_design, verbose=TRUE)
 summary(data)

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