wormsPE: ProteomicsExperiment with pulsed silac data from C. elegans...

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

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

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.