[R] replace zero in a matrix using random numbers

Yuan Chun Ding ycd|ng @end|ng |rom coh@org
Sat Jan 9 00:00:38 CET 2021

Hi Bert and Rui,

Thank you very much!  I had thought for every condition of  matrix ==0 ,  rnrom(n=1, 1, 0.1) will randomly generate a number with mean 1 and sd 0.1.


From: Bert Gunter [mailto:bgunter.4567 using gmail.com]
Sent: Friday, January 8, 2021 2:49 PM
To: Yuan Chun Ding <ycding using coh.org>
Cc: r-help using r-project.org
Subject: Re: [R] replace zero in a matrix using random numbers

?rnorm tells you that n, the first argument, is the number of observations/random numbers you wish to generate. You asked for 1.
So you need to ask for the number of 0's, something like:

> a <- matrix(rep(0:1, 3), nrow =3)
> a
     [,1] [,2]
[1,]    0    1
[2,]    1    0
[3,]    0    1
> a[!a] <- rnorm(sum(!a), 1,.1)
> a
          [,1]     [,2]
[1,] 0.8136788 1.000000
[2,] 1.0000000 1.146225
[3,] 0.9081908 1.000000


Bert Gunter

"The trouble with having an open mind is that people keep coming along and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Fri, Jan 8, 2021 at 2:33 PM Yuan Chun Ding <ycding using coh.org<mailto:ycding using coh.org>> wrote:
Hi R users,

I am analyzing miRNA sequence data for a special network analysis, I need to replace zero values in a matrix as random numbers with mean of 1 and standard deviation of 0.1.

er.miRCounts[er.miRCounts==0] <- rnorm(1,mean=1, sd=0.1);

this code made all zero values as 1.13, not random numbers across different zero values.  If all zero values in one row are replaced by the same 1.13,  then sd in that row is zero, causing other problem in the following calculation.

Can you help me?

Thank you,

Yuan chun Ding


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