sample_annotation {SWATH2stats} | R Documentation |
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.
sample_annotation(data, sample.annotation, data.type="OpenSWATH", column.file = "filename", change.run.id = TRUE, verbose=FALSE)
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. |
Returns a dataframe with each row annotated for the study design
Peter Blattmann
data("OpenSWATH_data", package="SWATH2stats") data("Study_design", package="SWATH2stats") data <- sample_annotation(OpenSWATH_data, Study_design)