Annotate Protein Information from Indra

This function annotates a data frame with protein information from Indra.

Usage

annotateProteinInfoFromIndra(df, proteinIdType)

Arguments

df

output of groupComparison function's comparisonResult table, which contains a list of proteins and their corresponding p-values, logFCs, along with additional HGNC ID and HGNC name columns

proteinIdType

A character string specifying the type of protein ID. It can be either "Uniprot" or "Uniprot_Mnemonic".

Value

A data frame with the following columns:

Protein

Character. The original protein identifier.

UniprotID

Character. The Uniprot ID of the protein.

HgncID

Character. The HGNC ID of the protein.

HgncName

Character. The HGNC name of the protein.

IsTranscriptionFactor

Logical. Indicates if the protein is a transcription factor.

IsKinase

Logical. Indicates if the protein is a kinase.

IsPhosphatase

Logical. Indicates if the protein is a phosphatase.

Examples

df <- data.frame(Protein = c("CLH1_HUMAN"))
annotated_df <- annotateProteinInfoFromIndra(df, "Uniprot_Mnemonic")
head(annotated_df)
#>      Protein UniprotId HgncId HgncName IsTranscriptionFactor IsKinase
#> 1 CLH1_HUMAN    Q00610   2092     CLTC                 FALSE    FALSE
#>   IsPhosphatase
#> 1         FALSE