Lego Sequencer
We had today again a ‘Bring your child to work ‘-day where we used the Lego Sequencer and I want to believe, it was again a success, as the kids liked it a lot (at least it seemed like it)
New publication
Our paper titled “Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus” just got published in the Journal of Animal Science:
https://academic.oup.com/jas/article/doi/10.1093/jas/skad333/7287507
Holiday read arrived
With the upcoming autumn holiday ahead, my autumn holiday read just arrived in time! Looking forward to having a light read, as my Python become a little rusty lately it is a nice kick-start again to read about it from an introductory perspective. First glance looks really nice!
Creating weighted tables with R / sum of numerics associated to some categorical variable
The normal table command table() calculates the frequency of each element of a vector like this:
R> df <- data.frame(var = c("A", "A", "B", "B", "C", "C", "C"))
R> table(df)
df
A B C
2 2 3 So, it tells us, we have two times A and B and three times C, accordingly.
However, if we have now the situation like this:
df <- data.frame(var = c("A", "A", "B", "B", "C", "C", "C"), value = c(10, 20, 20, 40, 15, 25, 35))Meaning, we have a categorical variable var and a numeric variable value and for each categorical variable we would like to get the sum over the numerical variable, we can simply use the base-R command aggregate like this
R> aggregate(value ~ var, data = df, FUN = sum)
var wt
1 A 40
2 B 60
3 C 70As I often use also the data.table package, here is also a simple solution using this package, assuming we do (respective have a data table from some other source, like fread)
library("data.table")
dt <- data.table(df)Then we can just sume over a column name with respect to another column like this (and assign the value into a new variable tot) :
setDT(dt)[, .(n = sum(value)), var]
Couldn’t delete a failed R package installation
Today I faced a strange thing, while I tried to install an update to one of my R-packages. As usually, I installed the latest version from it like this
library("devtools")
install_github("fischuu/GenomicTools")But the installation failed, and when I tried to reinstall it, I got this error message:
Installing package into ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
ERROR: failed to lock directory ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1’ for modifying
Try removing ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1/00LOCK-GenomicTools’
Warning message:
In i.p(...) :
installation of package ‘/tmp/Rtmp<...>Lv/file3c36<...>34/GenomicTools_0.2.11.tar.gz’ had non-zero exit statusSo, I tried to go in said directory and delete the folder manually and there I received another error:
rm: cannot remove '00LOCK-GenomicTools/GenomicTools/libs/.nfs00000001002e2<...>d': Device or resource busyI tried this and this, but nothing helped to delete that folder, it kept mocking my that the device is busy. Eventually, it helped just to rename the folder list this
mv 00LOCK-GenomicTools/ 00LOCK-GenomicTools-deleteThis/It is now still hanging there in the folder, but I was able to reinstall the R-package and now I need to revisit the folder in a few days and check, if the device is still busy or if I can delete it then…