[R] how to use vectorization instead of for loop
Stephen HK WONG
honkit at stanford.edu
Mon Mar 21 21:34:15 CET 2016
So much thanks Rui, the code can be so simple and fast.
By the way, ifelse is good for two conditions, in my case, either >0, or <0, I found there's a lot of row with value "Inf", I want to keep it in new column, how do I do that using ifelse ?
Thanks.
________________________________________
From: ruipbarradas at sapo.pt <ruipbarradas at sapo.pt>
Sent: Monday, March 21, 2016 11:50 AM
To: Stephen HK WONG
Cc: r-help at r-project.org
Subject: Re: [R] how to use vectorization instead of for loop
Hello,
I've renamed your dataframe to 'dat'. Since ?ifelse is vectorized, try
dat[, 4] <- ifelse(dat[, 2] > 0, 1 * (1/dat[,3]), -1* (1/dat[,3]))
Oh, and why do you multiply by 1 and by -1?
It would simply be 1/dat[,3] and -1/dat[,3].
Hope this helps,
Rui Barradas
Quoting Stephen HK WONG <honkit at stanford.edu>:
> Dear All,
>
>
> I have a dataframe like below but with many thousands rows,
>
> structure(list(gene_id = structure(1:6, .Label = c("0610005C13Rik",
> "0610007P14Rik", "0610009B22Rik", "0610009L18Rik", "0610009O20Rik",
> "0610010B08Rik,OTTMUSG00000016609"), class = "factor"),
> log2.fold_change. = c(0.0114463,
> -0.0960262, 0.00805151, -0.179981, -0.0629098, 0.155979), p_value = c(1,
> 0.77915, 0.98265, 0.68665, 0.85035, 0.72235), new.value = c("NA",
> "NA", "NA", "NA", "NA", "NA")), .Names = c("gene_id", "log2.fold_change.",
> "p_value", "new.value"), row.names = c(NA, 6L), class = "data.frame")
>
>
> I want to check if second column is positive or negative value, then
> I will do some calculation and put the new value in last column. I
> can do this with for loop like below but it is not efficient. Is
> there a better way to use a vectorization method instead of loop?
> Many thanks!
>
>
> for (i in 1:nrow(dataframe)) {
>
> if dataframe[i, 2]>0 {
>
> dataframe[i, 4]<- 1 * (1/dataframe[i,3])} else{
>
> dataframe[i, 4] <- -1* (1/dataframe[i,3])}
>
> }
>
>
> -------------------------------------------------------
>
> Stephen H.K. WONG, PhD.
>
> Stanford University
>
> [[alternative HTML version deleted]]
>
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