Description Usage Arguments Value Examples
Takes a list of thermo MSF files, parses and combines them into a single data frame, and computes areas for each protein group based on the top 3 method of quantitation.
1 | quantitate(reps, normalize = T, match_peps = T, relabel = c())
|
reps |
Vector. List of thermo MSF file names |
normalize |
Boolean. Should we normalize peptide areas for technical replicate to the total areas in a given replicate? |
match_peps |
Boolean. Should we quantitate only on matching peptides across technical replicates? |
relabel |
Named vector for relabeling protein groups. Names correspond to a pattern or string to match (i.e. the name or ID of a protein group), and values correspond to the new value (i.e. new protein group name). |
A data frame containing area information for all proteins.
protein_desc |
protein description |
area_mean |
average peptide area |
area_sd |
peptide area standard deviation |
peps_per_rep |
Number of peptides per technical replicate used to calculate |
1 2 3 | quantitate(c(parsemsf_example("test_db.msf"),
parsemsf_example("test_db2.msf")),
relabel = c("NP_12345.1" = "NP_1000.1"))
|
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