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Tutorial: use deseq2 in asthma
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gravatar for krwyaong.ju
12 weeks ago by
krwyaong.ju0 wrote:

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

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by krwyaong.ju0

> 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 REPLYlink written 12 weeks ago by krwyaong.ju0

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 REPLYlink written 12 weeks ago by Michael Love18k

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 REPLYlink written 12 weeks ago by krwyaong.ju0

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 REPLYlink written 12 weeks ago by thokall110

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 REPLYlink modified 12 weeks ago • written 12 weeks ago by Michael Love18k
0
gravatar for Michael Love
12 weeks ago by
Michael Love18k
United States
Michael Love18k wrote:

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

install.packages("here")
ADD COMMENTlink written 12 weeks ago by Michael Love18k
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