extractSDRF: Extract experimental design from MSstats format into SDRF...

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

Extract experimental design from MSstats format into SDRF format

Description

Extract experimental design from MSstats format into SDRF format

Usage

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

Arguments

data	MSstats formatted data that is the output of a dedicated converter, such as 'MaxQtoMSstatsFormat', 'SkylinetoMSstatsFormat', ect.
run_name	Run column name in SDRF data
condition_name	Condition column name in SDRF data
biological_replicate	Biological replicate column name in SDRF data
fraction	Fraction column name in SDRF data (if applicable). Default is 'NULL'. If there are no fractions keep 'NULL'.
meta_data	A data.frame including any additional meta data for the SDRF file that is not included in MSstats. This meta data will be added into the final SDRF file. Please ensure the run names in the meta data matches the run names in the MSstats data.

Examples

mq_ev = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv",
                                      package = "MSstatsConvert"))
mq_pg = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_pg.csv",
                                      package = "MSstatsConvert"))
annot = data.table::fread(system.file("tinytest/raw_data/MaxQuant/annotation.csv",
                                      package = "MSstatsConvert"))
maxq_imported = MaxQtoMSstatsFormat(mq_ev, annot, mq_pg, use_log_file = FALSE)
head(maxq_imported)

SDRF_file = extractSDRF(maxq_imported)

MeenaChoi/MSstats documentation built on Nov. 10, 2024, 2:43 p.m.