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Summarize PAnalyzer Results

summary.panalyzer.Rd

Provides a summary of the PAnalyzer results by grouping the data based on whether a protein is a target or decoy, and by its protein type. The summary includes the number of distinct proteins and protein groups for both target and decoy entries.

Usage

# S3 method for class 'panalyzer'
summary(object, ...)

Arguments

object

A data frame containing the results from the panalyzer function. This data frame must contain the following columns:

  • isDecoy: Logical indicator of whether the protein is a decoy (TRUE) or a target (FALSE).

  • proteinType: The type of protein as classified by PAnalyzer (e.g., "conclusive", "indistinguishable", "ambiguous", "non-conclusive").

  • proteinRef: Protein reference identifier.

  • groupRef: Protein group reference.

...

Additional arguments (currently ignored).

Value

A data frame summarizing the PAnalyzer results with the following columns:

  • Type: The type of protein ("conclusive", "indistinguishable", "ambiguous", "non-conclusive").

  • TargetProteins: The number of target proteins of the given type.

  • DecoyProteins: The number of decoy proteins of the given type.

  • TargetGroups: The number of target protein groups of the given type.

  • DecoyGroups: The number of decoy protein groups of the given type.