groupMemberPeptides: Peptide info for protein group members

In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

For a given reporter protein group identifier, information on its peptides is returned. It contains information on how the peptides are shared and in which member they occur.

Usage

groupMemberPeptides(x, reporter.protein.g, ordered.by.pos = TRUE, only.first.pos = TRUE)

Arguments

x	ProteinGroup object
reporter.protein.g	group reporter protein
ordered.by.pos	if TRUE, start position of peptides in proteins is exported and peptides are ordered by position
only.first.pos	if TRUE, only first occurence of peptide in protein is reported

Value

list of two: [1] peptide.info: data.frame peptide specificity n.shared.groups n.shared.proteins start.pos [2] group.member.peptides: data.frame each column corresponds to a group member, and each row to a peptide

Author(s)

Florian P Breitwieser

Examples

    data(ibspiked_set1)
    protein.group <- proteinGroup(ibspiked_set1)
    ceru.rat <- protein.g(protein.group,"CERU_RAT")
    groupMemberPeptides(protein.group,ceru.rat)

## find protein groups with members
    t <- table(proteinGroupTable(protein.group)$reporter.protein)
    t[t>2]
    protein.g <- names(t)[t>2][1]
    groupMemberPeptides(protein.group,protein.g)

isobar documentation built on Nov. 8, 2020, 7:48 p.m.