wrMisc: closeMatchMatrix – R documentation

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closeMatchMatrix

Reorganize results of search for close (similar) values in matrix-view

Description

closeMatchMatrix reorganizes/refines results from simple search of similar values of 2 sets of data by findCloseMatch (as list for one-to many relations) to more human friendly/readable matrix. This function returns results combining two sets of data which were initially compared (eg measured and threoretical values) as matrix-view using output of findCloseMatch and both original datastes Additional information (covariables, annotation, ...) may be included as optional columns for either 'predMatr' or 'measMatr'. Note : It is important to run findCloseMatch with sortMatch=FALSE ! Note : Results presented based on view of 'predMatr', so if multiple 'measMatr' are at within tolared distance, lines of 'measMatr' will be repeated; Note : Distances 'disToMeas' and 'ppmToPred' are oriented : neg value if measured is lower than predicted (and pos values if higher than predicted); Note : Returns NULL when nothing within given limits of comparison;

Usage

closeMatchMatrix(
  closeMatch,
  predMatr,
  measMatr,
  prefMatch = c("^x", "^y"),
  colPred = 1,
  colMeas = 1,
  limitToBest = TRUE,
  asDataFrame = FALSE,
  origNa = TRUE,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

`closeMatch`	(list) output from `findCloseMatch`, ie list with hits for each 'x' (1st argument) : named vectors of value & x index in name; run with 'sortMatch'=F
`predMatr`	(vector or matrix) predicted values, the column 'colPred' indicates which column is used for matching from `findCloseMatch`; if column 'id' present this column will be used as identifier for matching
`measMatr`	(vector or matrix) measured values, the column 'colMeas' indicates which column is used for matching from `findCloseMatch`; if column 'id' present this column will be used as identifier for matching
`prefMatch`	(character, length=2) prefixes ('^x' and/or '^y') thay may have been added by `findCloseMatch`
`colPred`	(integer or text, length=1) column of 'predMatr' with main values of comparison
`colMeas`	(integer or text, length=1) column of 'measMatr' with main measures of comparison
`limitToBest`	(integer) column of 'measMatr' with main measures of comparison
`asDataFrame`	(logical) convert results to data.frame if non-numeric matrix produced (may slightly slow down big results)
`origNa`	(logical) will try to use original names of objects 'predMatr','measMatr', if they are not multi-column and not conflicting other output-names (otherwise 'predMatr','measMatr' will appear)
`silent`	(logical) suppress messages
`callFrom`	(character) allows easier tracking of message(s) produced
`debug`	(logical) for bug-tracking: more/enhanced messages

Value

results as matrix-view based on initial results from findCloseMatch, including optional columns of suppelemental data for both sets of data for comparison. Returns NULL when nothing within limits

Examples

aA <- c(11:17); bB <- c(12.001,13.999); cC <- c(16.2,8,9,12.5,15.9,13.5,15.7,14.1,5)
(cloMa <- findCloseMatch(aA,cC,com="diff",lim=0.5,sor=FALSE))       
# all matches (of 2d arg) to/within limit for each of 1st arg ('x'); 'y' ..to 2nd arg = cC
(maAa <- closeMatchMatrix(cloMa,aA,cC,lim=TRUE))  #
(maAa <- closeMatchMatrix(cloMa,aA,cC,lim=FALSE,origN=TRUE))  #
(maAa <- closeMatchMatrix(cloMa,cbind(valA=81:87,aA),cbind(valC=91:99,cC),colM=2,
  colP=2,lim=FALSE))
(maAa <- closeMatchMatrix(cloMa,cbind(aA,valA=81:87),cC,lim=FALSE,deb=TRUE))  #
a2 <- aA; names(a2) <- letters[1:length(a2)];  c2 <- cC; names(c2) <- letters[10+1:length(c2)]
(cloM2 <- findCloseMatch(x=a2,y=c2,com="diff",lim=0.5,sor=FALSE)) 
(maA2 <- closeMatchMatrix(cloM2,predM=cbind(valA=81:87,a2),measM=cbind(valC=91:99,c2),
  colM=2,colP=2,lim=FALSE,asData=TRUE)) 
(maA2 <- closeMatchMatrix(cloM2,cbind(id=names(a2),valA=81:87,a2),cbind(id=names(c2),
  valC=91:99,c2),colM=3,colP=3,lim=FALSE,deb=FALSE))

wrMisc

Analyze Experimental High-Throughput (Omics) Data

v1.5.4

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release