value outside range from column in R dataframe

Question

Edit with example**

gene    pvalue    log2FoldChange
a        1         -1.5
b        0.01      -2
c        0.004      1.4

I have a dataframe like this ^^

I want to specify a cutoff for pvalue and a range for log2FoldChange outside of which I want the values. So I want ones which have a log2FoldChange >1 or <-1 and a pvalue of <0.05 I've tried:

res <- res[res$padj < 0.05 & res$log2FoldChange > 1 & res$log2FoldChange < -1,] 
res <- res[complete.cases(res), ]

But this didn't work! Gave me an empty dataframe called res.

Would be easier to help you if you had an reproducible example: https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example — s_baldur, Jul 20 '17 at 16:23
Looks like the first one is missing a comma, should at least be `res <- res[res$padj < 0.05 & res$log2FoldChange > 1 & res$log2FoldChange < -1,]` — Matt Tyers, Jul 20 '17 at 16:31

score 1 · Accepted Answer · answered Jul 20 '17 at 16:38

res$log2FoldChange > 1 & res$log2FoldChange < -1 is impossible. Hence, the empty set is returned. If you want a p-value cut-off and values outside a range of the other variable maybe what you really mean is the following.

inx1 <- res$padj < 0.05 & res$log2FoldChange > 1
inx2 <- res$padj < 0.05 & res$log2FoldChange < -1

res <- res[inx1 | inx2, ]
res <- res[complete.cases(res), ]

Obviously, this is completeky untested, since you've posted no data.

score 0 · Answer 2 · answered Jul 20 '17 at 16:33

0

You may try this (I assume you want log2FoldChange to lie in the interval R - (-1,1)

res[which(res$padj < 0.05 & (res$log2FoldChange > 1 || res$log2FoldChange< -1)),]

answered Jul 20 '17 at 16:33

Raj Padmanabhan

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no, sorry, for clarity, i want log2FoldChange less than -1 or greater than +1 – ainebrowne Jul 20 '17 at 16:37
Yes, that's the interval I implemented. – Raj Padmanabhan Jul 20 '17 at 16:42
@RajPadmanabhan: You're basically right, but I believe you wanted `|`, not `||`. From the help page of logic operators we see that the long form examines "only the first element of each vector". – Rui Barradas Jul 21 '17 at 06:47

value outside range from column in R dataframe

2 Answers2