Entering edit mode
krwyaong.ju
•
0
@krwyaongju-15652
Last seen 6.5 years ago
Dear Michael Love,
I am interested in your github; https://github.com/mikelove/asthma/blob/master/scripts/asthma.Rmd
I installed all packages as your guidelines (https://angus.readthedocs.io/en/2017/deseq2-asthma.html)
now I am running your scripts on Ubuntu16.04.
list.files("../data/quants/") .... ok
library(here) .... .... I can't find this package in r library installed.
can you help I can go further? Must I install "here"? and then next ... still not working????
with kind regards,
Jue
> list.files("../data/quants/")
character(0)
> list.files("/home/jkr/asthma/data/quants/")
[1] "SRR1565926" "SRR1565927" "SRR1565928" "SRR1565929" "SRR1565930"
[6] "SRR1565931" "SRR1565932" "SRR1565933" "SRR1565934" "SRR1565935"
[11] "SRR1565936" "SRR1565937" "SRR1565938" "SRR1565939" "SRR1565940"
[16] "SRR1565941" "SRR1565942" "SRR1565943" "SRR1565944" "SRR1565945"
[21] "SRR1565946" "SRR1565947" "SRR1565948" "SRR1565949"
> library(here)
here() starts at /root
> list.files(here("data","quants","SRR1565926"))
character(0)
>
how to write the right script after library(here)?
here() will find the correct root if your current working directory is somewhere in the asthma directory. In RStudio you can set the current directory to the source file location.
I 've done. seems no need of "here", I gave the correct path without writing "here" in your scripts.
another question; how to install "GenomeFeatures". many tries but failed. how to do?
You will likely get better answers if you show the code you have tried so far and the errors that it generates. If you mean the package Genomicfeatures you should be able to follow the instructions at https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html
If you hit a problem, make sure you've typed everything in exactly correct. You can always copy paste to avoid spelling mistakes, e.g.
then copy the name of the missing package
install.packages("<paste>")