labelRowsParam: List labelRows & reduceTable Defaults

View source: R/params.R

labelRowsParamR Documentation

List labelRows & reduceTable Defaults

Description

List of default parameters for combinedTable row annotation and removal. See help(labelRows) or ?labelRows for more details. reduceTableParam loads parameters for the more automated reduceTable function

Usage

labelRowsParam(
  useID = FALSE,
  maxRankX = 3,
  maxRankY = 3,
  minScore = 0.5,
  method = "score",
  delta = 0.1,
  maxRTerr = 10,
  resolveConflicts = FALSE,
  rtOrder = TRUE,
  remove = FALSE,
  balanced = TRUE,
  brackets_ignore = c("(", "[", "{")
)

reduceTableParam(
  useID = FALSE,
  maxRankX = 2,
  maxRankY = 2,
  minScore = 0.5,
  maxRTerr = 10,
  delta = 0.1,
  rtOrder = TRUE,
  method = "score",
  brackets_ignore = c("(", "[", "{")
)

Arguments

useID

option to annotate identity-matched strings as IDENTITY; default: FALSE

maxRankX

maximum rank allowable for X features

maxRankY

maximum rank allowable for Y features

minScore

minimum score threshold; default: 0.5

method

thresholding method for subgroup detection ("score" or "mzrt"); default: "score"

delta

score distance or mz/rt difference tolerances for subgrouping; default: 0.1

maxRTerr

maximum allowable difference between predicted RT (rtProj) & observed RT (rty); default: 10 minutes

resolveConflicts

logical. If TRUE, automatically resolves subgroups to 1-1 feature pair alignments

rtOrder

logical. If TRUE and resolveConflicts is TRUE, imposes retention order condition on paired alignments

remove

option to eliminate rows determined as removable; default: FALSE

balanced

option to reduce balanced groups; default: TRUE

brackets_ignore

bracket types for ignoring string comparisons

Value

list of labelRows parameters

See Also

labelRows, metabCombine, batchCombine, reduceTable

Examples

lrParams <- labelRowsParam(maxRankX = 2, maxRankY = 2, delta = 0.1,
                             maxRTerr = 0.5)


hhabra/Combiner documentation built on May 26, 2024, 5:08 p.m.