pdat_ {canprot}R Documentation

Get Protein Data

Description

Get data on protein expression and chemical composition.

Usage

  pdat_CRC(dataset = NULL, basis = "AA")

Arguments

dataset

character, specifies which dataset to retrieve

basis

character, keyword for basis species to use

Details

The pdat_ functions read CSV data files for data on relatively up- and down-expressed proteins reported in proteomic experiments, then uses protcomp to calculate some chemical compositional metrics.

pdat_CRC retrieves data for protein expression in colorectal cancer. Other pdat_ functions will be added in future versions of the package.

If dataset is NULL, the return value gives the names of all datasets that can be retrieved using this function. Each name indicates the study (publication) where the data were reported, constructed by combining the first characters of the (first three or four) authors' family names with the 2-digit year of publication. This coincides with the key-generation scheme used in some bibliography manager software. This abbreviation also corresponds the name of the CSV file containing the data. If more than one dataset is available from a single study (for example, for relative protein expression in different stages of cancer), dataset is suffixed by an underscore followed by a short abbreviation indicating the particular dataset.

Provide one of these names as the dataset argument to retrieve the data.

Value

A list consisting of dataset (the name of the dataset), basis (basis species used for the calculations), description (descriptive text), pcomp (compositional data generated by protcomp), up2 (logical vector with length equal to the number of proteins; TRUE if the protein is up-expressed in group 2 compared to group 1 (i.e. cancer compared to normal), FALSE otherwise), names (gene names for the proteins, if available).

See Also

get_pdat

Examples

data(canprot)
pdat_CRC()
pdat_CRC("JKMF10")  # same result as get_pdat("JKMF10")

[Package canprot version 0.0.2 Index]