Description Usage Arguments Value Examples
Extracts amino acid sequences (without post-translational modifications), assigned protein groups, and quality scores.
1 2 | make_pep_table(msf_file, min_conf = "High",
prot_regex = "^>([a-zA-Z0-9._]+)\\b", collapse = TRUE)
|
msf_file |
A file path to a ThermoFisher MSF file. |
min_conf |
"High", "Medium", or "Low". The minimum peptide confidence level to retrieve from MSF file. |
prot_regex |
Regular expression where the first group matches a protein name or ID from the protein description. Regex must contain ONE group. The protein description is typically generated from a fasta reference file that was used for the database search. |
collapse |
If TRUE, peptides that match to multiple protein sequences are collapsed into a single row with multiple protein descriptions and protein IDs in the |
A data frame of all peptides above the confidence cut-off from a ThermoFisher MSF file.
peptide_id |
a unique peptide ID |
spectrum_id |
a unique spectrum ID |
protein_id |
unique protein group ID to which this peptide maps |
protein_desc |
protein description from reference database used to assign peptides to protein groups, parsed according to |
sequence |
amino acid sequence (does not show post-translational modifications) |
pep_score |
PEP score |
q_value |
Q-value score |
1 2 3 4 5 6 7 8 9 10 11 | # Read from a path
make_pep_table(parsemsf_example("test_db.msf"))
# Retrieve full protein description
make_pep_table(parsemsf_example("test_db.msf"), prot_regex = "")
# ...which is also equivalent to...
make_pep_table(parsemsf_example("test_db.msf"), prot_regex = "^(.+)$")
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