CODEWITHSUNDEEP
rdataframefor-loopgsub
JPK
JPK

Reputation: 13

R: Nothing was replaced using gsub() function

Hi I've tried to replace value of columns in data frame using the following code.

sampleNumber <- c(1:length(sampleId))
for (value in sampleNumber){
  genotypeCol <- paste("annotateData$", sampleId[value], sep = "") #sampleId is a vector contains column names in annotateData
  genotypeCol <- gsub("0\\/0", "ref", genotypeCol)
  genotypeCol <- gsub("0\\/1|0\\/2|0\\/3|1\\/2|1\\/3|2\\/3", "het", genotypeCol)
  genotypeCol <- gsub("1\\/1|2\\/2|3\\/3", "hom", genotypeCol)
}

Anyway, the content are still the same, but it works fine if I use the following code instead.

annotateData$Genotype_SM01 <- gsub("0\\/0", "ref", annotateData$Genotype_SM01)
annotateData$Genotype_SM01 <- gsub("0\\/0", "ref", annotateData$Genotype_SM01)
annotateData$Genotype_SM01 <- gsub("0\\/0", "ref", annotateData$Genotype_SM01)

So any ideas to for this issue.

Upvotes: 1

Views: 49

Answers (1)

boski
boski

Reputation: 2467

You are feeding gsub() with a character string containing your variable name. To get the actual variable , use get(paste("annotateData$", sampleId[value], sep = ""))
Edit 

aux=get("annotateData")
var=aux[,sampleID[value]]

In this case, var holds the value of annotateData$Genotype_SM01

edit 2
reworking your problem, the following code should do what you want.

annotateData=data.frame("Genotype_SM01"=c("a","a","b"),
                    "Genotype_SM02"=c("a","a","a"),
                    "Genotype_SM02"=c("b","b","a"),
                    stringsAsFactors = FALSE)
sampleId=names(annotateData)

sampleNumber <- c(1:length(sampleId))

for (value in sampleNumber){
  aux=annotateData[,sampleID[value]]
  aux <- gsub("0\\/0", "ref", aux)
  aux <- gsub("0\\/1|0\\/2|0\\/3|1\\/2|1\\/3|2\\/3", "het", aux)
  aux <- gsub("1\\/1|2\\/2|3\\/3", "hom", aux)
  annotateData[,sampleID[value]]=aux
}

Upvotes: 1

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