get_parsimony_pep2prot | R Documentation |
Wrapper function to read in infiles, identify the parsimonious proteins to account for the peptides and then (optionally) compare the new and old master protein assignments
get_parsimony_pep2prot(
infiles,
seq_col = "Sequence",
prot_col = "Protein.Accessions",
master_prot_col = "Master.Protein.Accessions",
compare_old_new = TRUE
)
infiles |
|
seq_col |
|
prot_col |
|
master_prot_col |
|
compare_old_new |
|
Returns an data.frame
object which maps peptide sequences to
consensus master protein ID(s)
## Not run:
# The input in this example is 2x peptideGroups.txt outputs from Proteome
# Discoverer. Both files must have the columns (cols) specified. This may require
# re-exporting the peptideGroups.txt file from PD as the "Protein.Accessions"
# column is often not there by default.
get_parsimony_pep2prot(
list("peptideGroups1.txt", "peptideGroups2.txt"),
seq_col = "Sequence",
prot_col = "Protein.Accessions",
master_prot_col = "Master.Protein.Accessions",
compare_old_new = TRUE
)
## End(Not run)
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