lcb3_4: Data for exercise 4

In lgatto/QFeaturesScpWorkshop2021: Reproducing a single-cell proteomics data analysis using QFeatures and scp

Description

A QFeatures object that has been generated to run exercise 4. It was generated from the v02-scp.Rmd vignette that replicates the SCoPE2 data processing workflow for batch LCB3 up to batch correction. This dataset can be used to demonstrate how to add SingleCellExperiment objects as new assay in a QFeatures object and create links with a parent assay.

lcb3_4 contains 55 assays:

• Assay 1-24: PSM data for 24 MS runs

• Assay 25-48: aggregated peptide data for 24 MS runs

• Assay 49: joined peptide data containing the sample of all 24 MS runs

• Assay 50: peptide data after a first normalization

• Assay 51: peptide data after a second normalization

• Assay 52: peptide data after log-transformation

• Assay 53: aggregated protein data

• Assay 54: protein data after a first normalization

• Assay 55: protein data after a second normalization and imputation of missing data

sce corresponds to Assay 55 after batch correction using ComBat.

Usage

data("lcb3_4")

Format

An object of class QFeatures of length 55.

See Also

Other exercise datasets are available: lcb3_1, lcb3_2, lcb3_3, lcb3_5.

lgatto/QFeaturesScpWorkshop2021 documentation built on Dec. 21, 2021, 10:44 a.m.