TCGAretriever (version 1.5)

get_protein_info: Retrieve Information on Antibodies Used for Protein Levels Determination

Description

Retrieve information on antibodies used by reverse-phase protein arrays (RPPA) to measure protein/phosphoprotein levels.

Usage

get_protein_info(csid = NULL, array_type = "protein_level",
  glist = NULL)

Value

data frame having one antibody per row and four columns

Arguments

csid

String corresponding to the Cancer Study Identifier

array_type

String, c("protein_level", "phosphorylation"). Retrieve information about antibodies used for detecting total protein levels or phosphorilated levels of the protein product of the gene of interest

glist

Character vector including one or more gene identifiers (ENTREZID or OFFICIAL_SYMBOL)

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

info1 <- get_protein_info("blca_tcga", glist = c("TP53", "PTEN", "E2F1", "AKT1"))
if (nrow(info1) > 0) {
  message("Total protein levels information")
  info1
} else {
  message("Server may be down, please try again later...")
}
#
info2 <- get_protein_info("blca_tcga", "phosphorilation", c("TP53", "PTEN", "E2F1", "AKT1"))
if (nrow(info2) > 0) {
  message("Phospho-protein levels information")
  info2
} else {
  message("Server may be down, please try again later...")
}