closeMatchMatrix: Reorganize results of search for close (similar) values in...

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

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

See Also

findCloseMatch, checkSimValueInSer

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 documentation built on Nov. 17, 2023, 5:09 p.m.