Tutorial:use deseq2 in asthma
1
0
Entering edit mode
@krwyaongju-15652
Last seen 3.2 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

deseq2 Tutorial • 1.0k views
ADD COMMENT
0
Entering edit mode

> 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)?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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. 

> library(GenomicFeatures)
Error in library(GenomicFeatures) : there is no package called ‘GenomicFeatures’

then copy the name of the missing package

install.packages("<paste>")
ADD REPLY
0
Entering edit mode
@mikelove
Last seen just now
United States

You need to install "here" first. Because this is a CRAN package, you can do:

install.packages("here")
ADD COMMENT

Login before adding your answer.

Traffic: 503 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6