TCGAretriever (version 1.5)

get_protein_data: Retrieve Protein Expression Data from a TCGA Study

Description

TCGA includes Information about Protein Expression measured by reverse-phase protein arrays. Antibody Information can be exported together with Expression Data. All expression data will be retrieved for all available protein targets.

Usage

get_protein_data(case_id = NULL, array_info = TRUE)

Value

Data Frame with one gene (protein target) per row

Arguments

case_id

String corresponding to the Identifier of the Case List of Interest

array_info

Logical. If TRUE, Antibody Information will also be exported

Author

Damiano Fantini,

References

• http://www.biotechworld.it/bioinf/2016/07/11/tcga-data-via-tcgaretriever/

• https://www.data-pulse.com/dev_site/TCGAretriever/

Examples

# Protein Expression Only
blca_protein <- get_protein_data("blca_tcga_sequenced", FALSE)
if (nrow(blca_protein) > 10 & ncol(blca_protein) > 8) {
  blca_protein[1:8,1:8]
} else {
  message("Server may be down, please try again later...")
}
#
# Example including Antibody Information
blca_protein <- get_protein_data("blca_tcga_sequenced", TRUE)
if (nrow(blca_protein) > 10 & ncol(blca_protein) > 8) {
  blca_protein[1:8,1:8]
} else {
  message("Server may be down, please try again later...")
}