example_proteome {proBatch} | R Documentation

## Example protein data in long format

### Description

This is OpenSWATH-output data from Aging study with all iRT, spike-in peptides, few representative peptides and proteins for signal improvement demonstration. Using `matrix_to_long` can be converted to `example_proteome_matrix`

### Usage

    example_proteome

### Format

A data frame with 124655 rows and 7 variables:

peptide_group_label

  peptide ID, which is regular feature level. This column is mostly used as `feature_id_col`

used for merging with `"example_peptide_annotation"`

Intensity

  peptide group intensity in given sample. Used in function as `measure_col`

Protein

  Protein group ID, specified as N/UniProtID1|UniProtID2|..., where N is number of protein peptide group maps to. If 1/UniProtID, then this is proteotypic peptide, in functions used as `protein_col`

FullRunName

  name of the file, in most functions used for `sample_id_col`

m_score

  column marking the quality of peptide IDs, used as `qual_col` throughout the script; when `qual_value` is 2 in this column, peptide has been imputed (requantified)

...

### Source

PRIDE ID will be added upon the publication of the dataset

[Package proBatch version 1.11.0 Index]