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

View source: R/SDRFconverter.R

SDRFtoAnnotationR Documentation

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 July 13, 2024, 10:59 a.m.