R version 4.5.0 RC (2025-04-04 r88118 ucrt) -- "How About a Twenty-Six"
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> ###
> ### NEEDLES.R - Package test code
> ###
> 
> options(warn=1)
> library(NameNeedle)
> source("checkFuncs")
> 
> extdata.dir <- system.file("extdata", package="NameNeedle")
> data(cellLineNames)
> 
> 
> ## Change the default settings...
> needleParams <- defaultNeedleParams
> needleParams$MISMATCH <- -2
> needleParams$MATCH <- 2
> 
> ## Match RPPA names to SF2 names
> matchscore <- matchcode <- rep(NA, length(sf2Names))
> for (j in seq_along(sf2Names)) {
+     scores <- sapply(rppaNames,
+                      function(x, y) {
+                          needles(x, y, needleParams)$score
+                      },
+                      y=sf2Names[j])
+     matchcode[j] <- paste(which(scores == max(scores)), collapse=',')
+     matchscore[j] <- max(scores)
+ }
> 
> rppaMatch <- sapply(matchcode,
+                     function(x) {
+                         y <- as.numeric(strsplit(x, ',')[[1]])
+                         paste(rppaNames[y], collapse="; ")
+                     })
> 
> ## Match Illumina names to SF2 names
> imatchscore <- imatchcode <- rep(NA, length(sf2Names))
> for (j in seq_along(sf2Names)) {
+     scores <- sapply(illuNames,
+                      function(x, y) {
+                          needles(x, y, needleParams)$score
+                      },
+                      y=sf2Names[j])
+     imatchcode[j] <- paste(which(scores == max(scores)), collapse=',')
+     imatchscore[j] <- max(scores)
+ }
>  
> illuMatch <- sapply(imatchcode,
+                     function(x) {
+                         y <- as.numeric(strsplit(x, ',')[[1]])
+                         paste(illuNames[y], collapse="; ")
+                     })
> 
> ## Collect aggregated output
> matcher <- data.frame(rppaMatch=rppaMatch,
+                       rppaScore=matchscore,
+                       illuMatch=illuMatch,
+                       illuScore=imatchscore,
+                       stringsAsFactors = TRUE)
> 
> ## Save results to disk (uncomment iff code changed)
> prevResults.filename <- "namesMatched.tsv"
> # uncomment iff code changed - replace existing results manually
> #write.table(matcher, file=prevResults.filename, sep='\t', quote=FALSE, col.names=NA)
> 
> ## Retrieve previous results
> prevResults <- local({
+     prevResults.pathname <- file.path(extdata.dir, prevResults.filename)
+     colClasses <- c("integer", rep(c("factor", "numeric"), 2))
+     df <- read.delim(prevResults.pathname, colClasses=colClasses,
+                      header=TRUE, stringsAsFactors = TRUE)
+     df[, -1]    ## Toss unwanted first column (row numbers)
+ })
> 
> ## Verify against previous results
> checkIdentical(matcher, prevResults)
[1] TRUE
> 
> 
> proc.time()
   user  system elapsed 
   7.48    0.09    7.57