labelRowsParam: List labelRows & reduceTable Defaults

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

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 June 5, 2024, 10:56 a.m.