SDRFtoAnnotation: Convert SDRF experimental design file into an MSstats...

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Convert SDRF experimental design file into an MSstats annotation file

Description

Takes an SDRF file and outputs an MSstats annotation file. Note the information in the SDRF file must be correctly annotated for MSstats so that MSstats can identify the experimental design. In particular the biological replicates must be correctly annotated, with group comparison experiments having a unique ID for each BioReplicate. For more information on this please see the Supplementary of the most recent MSstats paper

Usage

SDRFtoAnnotation(
  data,
  run_name = "comment[data file]",
  condition_name = "characteristics[disease]",
  biological_replicate = "characteristics[biological replicate]",
  fraction = NULL
)

Arguments

data	SDRF annotation file
run_name	Column name in SDRF file which contains the name of the MS run. The information in this column must match exactly with the run names in the PSM file
condition_name	Column name in SDRF file which contains information on the conditions in the data.
biological_replicate	Column name in SDRF file which contains the identifier for the biological replicte. Note MSstats uses this column to determine if the experiment is a repeated measure design. BioReplicte IDs should only be reused if the replicate was measured multiple times.
fraction	Column name in SDFT file which contains information on the fractionation in the data. Only required if data contains fractions. Default is 'NULL'

Examples

head(example_SDRF)

msstats_annotation = SDRFtoAnnotation(example_SDRF)

head(msstats_annotation)

MeenaChoi/MSstats documentation built on April 27, 2024, 7:18 p.m.