Limit mapping expansion to unmapped codes

[FearlessNewbie]

createUKBphenome/scripts/function.createUKBphenome.r

Lines 94 to 105 in dcc06c8

	mappedICD9Codes <- NULL
	icd9map_new <- list()
	for(i in 1:nrow(icd9map)){
	mapped9 <- grep(icd9map$ICD9[i],codeICD9)
	if(length(mapped9) > 0) {
	mappedICD9Codes <- unique(c(mappedICD9Codes,codeICD9[mapped9]))
	icd9map_new[[icd9map$ICD9[i]]] <- data.table(
	'phecode'=icd9map$PheCode[i],
	'ICD9'=codeICD9[mapped9])
	}
	}
	icd9key <- rbindlist(icd9map_new)

These codes are better applied only to ICD codes that are not successfully mapped, so as to prevent the creation of an excessive number of new ICD–phecode mappings.

notmappedcodeICD9 <- unique(codeICD9[!codeICD9 %in% icd9map$ICD9])

mappedICD9Codes <- NULL
icd9map_new <- list()
for (i in 1:nrow(icd9map)) {
pattern <- paste0("^", gsub("([][{}()+*^$|\\?.])", "\\\1", icd9map$ICD9[i]))
mapped9 <- grep(pattern, notmappedcodeICD9)
if (length(mapped9) > 0) {
mappedICD9Codes <- unique(c(mappedICD9Codes, notmappedcodeICD9[mapped9]))
icd9map_new[[icd9map$ICD9[i]]] <- data.table(
"phecode" = icd9map$phecode[i],
"ICD9" = notmappedcodeICD9[mapped9]
)
}
}

mappedcodeICD9 <- rbindlist(icd9map_new) %>% unique()