ccleProteome2SummarizedExperiment: Convenient access to the CCLE proteome data

In ccb-hms/BioPlex: R-side access to BioPlex protein-protein interaction data

Convenient access to the CCLE proteome data

Description

Functionality for storing the protein expression data from the Cancer Cell Line Encyclopedia (CCLE) in a SummarizedExperiment.

Usage

ccleProteome2SummarizedExperiment(df, cell.line = "HCT116")

Arguments

df	a data.frame storing the CCLE protein expression data with one measurement in each row. Typically obtained from ExperimentHub. See examples.
cell.line	character. One or more cell line IDs such as "HCT116" (human colon cancer cell line 116). Use NULL to not subset by cell line. Defaults to "HCT116", which will then subset the df to measurements for HCT116 only.

Value

A SummarizedExperiment storing protein expression data for the specified cell line(s).

References

CCLE proteomics: https://gygi.hms.harvard.edu/publications/ccle.html

Examples

  # Connect to ExperimentHub
  eh <- ExperimentHub::ExperimentHub()

  # Obtain CCLE proteome data frame
  AnnotationHub::query(eh, c("gygi", "depmap"))
  ccle.prot <- eh[["EH3459"]]
  ccle.prot <- as.data.frame(ccle.prot)

  # Turn into a SummarizedExperiment
  se <- ccleProteome2SummarizedExperiment(ccle.prot)
  

ccb-hms/BioPlex documentation built on Aug. 5, 2023, 9:15 p.m.