get_peptide_coverage: Creates the "Peptide Coverage" Object

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

Creates the "Peptide Coverage" Object

Description

Returns an object with two data tables used to visualize where identified peptides map to a specific literature sequence. These data tables include one that contains sequences with start and stop positions, and the other contains counts of identified residues.

Usage

get_peptide_coverage(ScanMetadata, ProteinTable, ProteinID)

Arguments

ScanMetadata	Object of the scan_metadata class from get_scan_metadata. Required.
ProteinTable	A "protein_table" object generated by get_protein_table. Required.
ProteinID	The ID of the protein to pull protein coverage information from. Required.

Details

The two outputted data tables are used by the three coverage plots.

The first is called "PeptidesByPosition" and is used by Coverage Plot and Coverage Lit Seq Plot.

Scan Number	MS Scan Number from ScanMetadata
Sequence	Peptide or protein sequence of the fragment or literature sequence.
Peptide Start Position	A single number to indicate where the fragment begins on the literature sequence (from N to C)
Q Value	The Q value (adjusted P value) of the peptide-spectral match provided by a database search tool.
Score	The score of the peptide-spectral match (typically a small value where smaller = better match)

The second is called "ResidueCount" and is used by coverage bar plot.

Residue	The residue from the literature sequence written in letter annotation and position format. i.e. "M1" is the first methionine.
Count	The number of times that residue was identified across all fragments.
Position	The residue's position on the literature sequence

Examples

## Not run: 

# Make Peptide Coverage Object
PeptideCoverage <- get_peptide_coverage(ScanMetadata = BU_ScanMetadata, ProteinTable = ProteinTable1, ProteinID = "SO_0225")


## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.