filterPSMs: Filter out unreliable PSMs.

In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

Filter out unreliable PSMs.

Description

Functions to filter out PSMs matching. The PSMs should be stored in a PSM such as those produced by PSM().

• filterPsmDecoy() filters out decoy PSMs, i.e. those annotated as isDecoy.

• filterPsmRank() filters out PSMs of rank > 1.

• filterPsmShared() filters out shared PSMs, i.e. those that match multiple proteins.

• filterPsmFdr() filters out PSMs based on their FDR.

Usage

filterPSMs(
  x,
  decoy = psmVariables(x)["decoy"],
  rank = psmVariables(x)["rank"],
  protein = psmVariables(x)["protein"],
  spectrum = psmVariables(x)["spectrum"],
  peptide = psmVariables(x)["peptide"],
  verbose = TRUE
)

filterPsmDecoy(x, decoy = psmVariables(x)["decoy"], verbose = TRUE)

filterPsmRank(x, rank = psmVariables(x)["rank"], verbose = TRUE)

filterPsmShared(
  x,
  protein = psmVariables(x)["protein"],
  peptide = psmVariables(x)["peptide"],
  verbose = TRUE
)

filterPsmFdr(x, FDR = 0.05, fdr = psmVariables(x)["fdr"], verbose = TRUE)

Arguments

x	An instance of class PSM.
decoy	character(1) with the column name specifying whether entries match the decoy database or not. Default is the decoy PSM variable as defined in psmVariables(). The column should be a logical and only PSMs holding a FALSE are retained. Filtering is ignored if set to NULL or NA.
rank	character(1) with the column name holding the rank of the PSM. Default is the rank PSM variable as defined in psmVariables(). This column should be a numeric and only PSMs having rank equal to 1 are retained. Filtering is ignored if set to NULL or NA.
protein	character(1) with the column name holding the protein (groups) protein. Default is the protein PSM variable as defined in psmVariables(). Filtering is ignored if set to NULL or NA.
spectrum	character(1) with the name of the spectrum identifier column. Default is the spectrum PSM variable as defined in psmVariables(). Filtering is ignored if set to NULL or NA.
peptide	character(1) with the name of the peptide identifier column. Default is the peptide PSM variable as defined in psmVariables(). Filtering is ignored if set to NULL or NA.
verbose	logical(1) setting the verbosity flag.
FDR	numeric(1) to be used to filter based on the fdr variable. Default is 0.05.
fdr	character(1) variable name that defines that defines the spectrum FDR (or any similar/relevant metric that can be used for filtering). This value isn't set by default as it depends on the search engine and application. Default is NA.

Value

A new filtered PSM object with the same columns as the input x.

Author(s)

Laurent Gatto

Examples

f <- msdata::ident(full.names = TRUE, pattern = "TMT")
basename(f)
id <- PSM(f)
filterPSMs(id)

rformassspectrometry/PSM documentation built on Dec. 13, 2024, 7:27 a.m.