wormsPE {pulsedSilac} | R Documentation

## ProteomicsExperiment with pulsed silac data from C. elegans strains

### Description

A pre-built `SilacProteomicsExperiment` object with data from a pulsed silac experiment done in C. elegans by Visscher et al. 2016. It only contains the data from the first 250 priteins and two old worms strains (OW40 and OW450).

### Usage

    data(wormsPE)

### Format

A `SilacProteomicsExperiment` object with 250 proteins and 3574 peptides in a total of 14 samples.

colData

  A `DataFrame` with the design of the experiment: samples, timepoints, replicates...

assaysProt

  A list of matrices with quantification data at protein level: total intensity (int_total), light isotope intensity (int_light), heavy isotope intensity (int_heavy) and heavy/light isotope intensty ratio (ratio).

rowDataProt

  A `DataFrame` with 22 columns that contains general protein information: ids, gene names, molecular weight...

assaysPep

  A list of matrices with quantification data at peptide level: total intensity (int_total), light isotope intensity (int_light), heavy isotope intensity (int_heavy) and heavy/light isotope intensty ratio (ratio).

rowDataPept

  A `DataFrame` with 46 columns that contains general protein information: ids, amino acids counts, length...

linkerDf

  A `data.frame` with 3574 rows and 4 columns. It contains the relationships between proteins and peptides in the ProteomicsExperiment object.

### Details

It is used as example in the pulsed silac vignette to illustrate the main data analysis functions and in the examples of the documentation.

### References

https://www.ncbi.nlm.nih.gov/pubmed/28679685

[Package pulsedSilac version 1.4.0 Index]