gene conversion microbenchmarking

library(Homo.sapiens)
library(hash)
library(org.Hs.eg.db)

DisplayName.1 <- function(NM){
  if(length(NM)>1)
    return(unlist(lapply(NM,DisplayName)))
  if(length(NM)==0)
    return("NA")
  #else; do one:
  j <- tryCatch(EG_to_Name(RefSeq_to_EG(NM)), error=function(e) NM )
  if( is.na(j) || nchar(j)<2 )
    j <- NM;
  return_or_null(j)
}

DisplayName.2 <- function(NMs)
  select(org.Hs.eg.db,keytype="REFSEQ",
         keys=NMs, multiVals="first",
         columns=c('SYMBOL'))$SYMBOL

DisplayName.3 <- function(NMs)
  select(Homo.sapiens, keys=NMs, keytype="REFSEQ",
         columns=c("SYMBOL"))$SYMBOL


refseqs = AnnotationDbi::keys(org.Hs.eg.db,keytype="REFSEQ")
roi5 <- sample(refseqs,5,replace=FALSE)
roi50 <- sample(refseqs,50,replace=FALSE)

#what if we pre-cache:
system.time( hash(refseqs, DisplayName.2(refseqs)) )
PRECACHE <- hash(refseqs, DisplayName.2(refseqs))
DisplayName.4 <- function(NMs) hash::values(PRECACHE[NMs])

res <- microbenchmark(DisplayName.1(roi5),
                      DisplayName.2(roi5),
                      DisplayName.3(roi5),
                      DisplayName.4(roi5), times=40L)
print(res)

res <- microbenchmark(DisplayName.1(roi50),
                      DisplayName.2(roi50),
                      DisplayName.3(roi50),
                      DisplayName.4(roi50),times=30L)
print(res)