pdat_ {canprot}R Documentation

Get Protein Expression Data

Description

Get differentially expressed proteins and amino acid compositions.

Usage

  pdat_breast(dataset = 2020)
  pdat_colorectal(dataset = 2020)
  pdat_liver(dataset = 2020)
  pdat_lung(dataset = 2020)
  pdat_pancreatic(dataset = 2020)
  pdat_prostate(dataset = 2020)
  pdat_hypoxia(dataset = 2020)
  pdat_secreted(dataset = 2020)
  pdat_3D(dataset = 2020)
  pdat_glucose(dataset = 2020)
  pdat_osmotic_bact(dataset = 2020)
  pdat_osmotic_euk(dataset = 2020)
  pdat_osmotic_halo(dataset = 2020)
  .pdat_multi(dataset = 2020)
  .pdat_osmotic(dataset = 2017)

Arguments

dataset

character, dataset name

Details

The pdat_ functions assemble lists of up- and down-regulated proteins and retrieve their amino acid compositions using protcomp. The result can be used with get_comptab to make a table of compositional metrics that can then be plotted with diffplot.

If dataset is 2020 (the default) or 2017, the function returns the names of all datasets in the compilation for the respective year.

Each dataset name starts with a reference key indicating the study (i.e. paper or other publication) where the data were reported. The reference keys are made by combining the first characters of the authors' family names with the 2-digit year of publication.

If a study has more than one dataset, the reference key is followed by an underscore and an identifier for the particular dataset. This identifier is saved in the variable named stage in the functions, but can be any descriptive text.

To retrieve the data, provide a single dataset name in the dataset argument. Protein expression data is read from the CSV files stored in extdata/expression/, under the subdirectory corresponding to the name of the pdat_ function. Some of the functions also read amino acid compositions (e.g. for non-human proteins) from the files in extdata/aa/.

Descriptions for each function:

Value

A list consisting of:

dataset

Name of the dataset

description

Descriptive text for the dataset, used for making the tables in the vignettes (see mkvig)

pcomp

UniProt IDs together with amino acid compositions obtained using protcomp

up2

Logical vector with length equal to the number of proteins; TRUE for up-regulated proteins and FALSE for down-regulated proteins

Examples

# List datasets in the 2017 complilation for colorectal cancer
pdat_colorectal(2017)
# Get proteins and amino acid compositions for one dataset
pdat_colorectal("JKMF10")

[Package canprot version 1.1.0 Index]