dbGetPeptideTable: get the paptide table belonging defined by PeptideIDs ot...

In BenBruyneel/proteinDiscover: ProteinDiscover

get the paptide table belonging defined by PeptideIDs ot proteinGroupIDs

Description

get the paptide table belonging defined by PeptideIDs ot proteinGroupIDs

Usage

dbGetPeptideTable(
  db,
  peptideIDs = NA,
  proteinGroupIDs = NA,
  columns = NA,
  masterProtein = TRUE,
  sortorder = NA,
  SQL = FALSE
)

Arguments

db	database access 'handle'
peptideIDs	the peptideIDs to be retrieved. This can be in numeric or character vector format OR the output from the dbGetPeptideIDs function (a data.frame with column "TargetPeptideGroupsPeptideGroupID")
proteinGroupIDs	the proteinGroupIDs usually come from the TargetProtein Table. This can be in numeric or character vector format. Note: if this parameter is not NA, then peptideIDs will be ignored. This makes it possible to retrieve the peptides belonging to a protein w/o first having to retrieve toe Peptide ID's
columns	allows the selection of columns to take from the table, default = NA (all columns)
masterProtein	use the IsMasterProtein column to be zero, default == TRUE. If more advanced filtering is needed, use db_getTable()
sortorder	allows for sorting of the selected columns, default = NA, (no sorting). Other valid values are a single character string ("ASC" or "DESC") or a character vector of the same length as the columnNames vector containing a series of "ASC" or "DESC"
SQL	allows the function to return the SQL query statement in stead of a data.frame

Value

a data.frame containing requested data from the peptide table or a character string specifying a SQL query

BenBruyneel/proteinDiscover documentation built on March 16, 2024, 4:36 p.m.