Keep rows with columns having values between -1 and 1 from a dataframe in R
2
1
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10 months ago

I have a dataframe in R that looks like this:

   V1         T1         T2         T3         T4        T5
  CXCL6  0.8536601  1.0903336  3.7633042  5.5800459 5.8477150
  PPBP  0.7739450  0.3587961  0.5073359  0.2743522 0.6221722
  CXCL10  0.1258370 -0.3535165 -0.7460387  3.5604672 0.1971432
  CXCL11 -0.2563139  0.7117200  0.0000000 -0.2288303 0.9955557
  CXCL12  0.6181279  1.7529310  1.7637760  1.2752787 1.2284810

I want to keep the rows that have values only between -1 and 1.

I have tried this command but unfortunately it does not work.

condition1 <- Genes[,c(2:6)] <=-1 & Genes[,c(2:6)] >=1
Genes <- Genes[condition1,]

Can someone tell me where I am wrong so that I can successfully filter my dataframe.

R • 1.1k views
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1
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Assuming these are log2 fold changes or something like that, I don't know why you would want columns with values between -1 and 1, because most people want values exactly outside of that range. I may be reading this wrong, but you also seem to be asking for values <=-1 which is to the "left" of -1, and >=1 which is to the "right" of 1.

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1
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Did you try && instead of & ?

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1
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Since the length(condition1) is >1, and && check only for the first element in vector, && should be avoided here.

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2
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10 months ago
Basti ▴ 920

Your condition is not clear, but if you want rows that contain values that are ONLY between -1 and 1, this should work :

Genes[which(rowSums(  (Genes[,2:6]>=-1) & (Genes[,2:6]<=1))==5),]
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0
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Thank you for your comment but unfotunately it did not work for me.

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0
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What do you mean by it did not work? Do you get an error or it doesn't do what you expect?

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didn't do what i expected unfortunately.

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2
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10 months ago

There should be more tidy way for that, but here is my solution.

rowIdx = as.numeric()
for(i in 1:nrow(Genes)){
  cond = Genes[-1][i,] >= -1 & Genes[-1][i,] <=1
  if(all(cond == TRUE)){
    rowIdx = c(rowIdx, i)
  }
}

Then subset your dataframe by rowIdx:

GenesSubset = Genes[rowIdx,]
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