I am pretty new to R and I have tried all of the suggested ways to access the data for the book, but each way has not worked. Is there any other way to access the data?

after correcting downloading and extracting data and when i run this below command, it shows error
what to do in this case?

enhancerFilePath=system.file("extdata",

•                          "subset.enhancers.hg18.bed",
  

•                          package="compGenomRData")
  

cpgiFilePath=system.file("extdata",

•                      "subset.cpgi.hg18.bed",
  

•                      package="compGenomRData")
  

read enhancer marker BED file

enh.df <- read.table(enhancerFilePath, header = FALSE)
Error in read.table(enhancerFilePath, header = FALSE) :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former

Dear Sir,

Thank you very much for making Computational genomics R. I liked it very much and going through all the chapters and exercises. I want to know where can I find the solutions for the exercises mentioned in the book. Kindly guide me. thanks in advance

> library(data.table)
> df.f=d(enhancerFilePath, header = FALSE,data.table=FALSE)

Error in d(enhancerFilePath, header = FALSE, data.table = FALSE) : 
  could not find function "d"

Function d() is also not available in data.table CRAN package documentation (https://cran.r-project.org/web/packages/data.table/data.table.pdf).

Is it supposed to be, df.f=fread(enhancerFilePath, header = FALSE,data.table=FALSE)?

> head(df.f)
     V1     V2     V3 V4   V5 V6    V7      V8 V9
1 chr20 266275 267925  . 1000  .  9.11 13.1693 -1
2 chr20 287400 294500  . 1000  . 10.53 13.0231 -1
3 chr20 300500 302500  . 1000  .  9.10 13.3935 -1
4 chr20 330400 331800  . 1000  .  6.39 13.5105 -1
5 chr20 341425 343400  . 1000  .  6.20 12.9852 -1
6 chr20 437975 439900  . 1000  .  6.31 13.5184 -1

Can you please clarify this?

When I tried to install compGenomeRData by using code:
devtools::install_github("compgenomr/compGenomRData")

I am getting this error:

Error: Failed to install 'compGenomRData' from GitHub: Does not appear to be an R package (no DESCRIPTION) In addition: Warning messages: 1: In utils::untar(tarfile, ...) : ‘tar.exe -xf "C:\Users\riYaz\AppData\Local\Temp\Rtmpkzp96L\fileb6c59027e80.tar.gz" -C "C:/Users/riYaz/AppData/Local/Temp/Rtmpkzp96L/remotesb6c41c63d88"’ returned error code 1 2: In system(cmd, intern = TRUE) : running command 'tar.exe -tf "C:\Users\riYaz\AppData\Local\Temp\Rtmpkzp96L\fileb6c59027e80.tar.gz"' had status 1

Hello,

For exercise 12 in section 2.10.3, I need 2 files, rn4.refseq.bed and rn4.refseq2name.txt. However, these are not present in extdata.

Downloading GitHub repo compgenomr/compGenomRData@master
Error: Failed to install 'compGenomRData' from GitHub:
incomplete block on file
In addition: Warning message:
closing unused connection 4 (compgenomr-compGenomRData-7a8279e/inst/extdata/CpGi.hg19.table.txt)

Hi there, error when trying to upload data, same issue reported 2 weeks ago

devtools::install_github("compgenomr/compGenomRData")
Downloading GitHub repo compgenomr/compGenomRData@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/compgenomr/compGenomRData/tarball/HEAD' failed

For exercise 6.6.3 question No. 1 you asked to view the promoters for chr20 in the H1.ESC.H3K4me1.chr20.bw file. But there is no file with that name.

Dear Dr. Alkalin,

I have two problems with your nice book:

1. can't install package with data:

devtools::install_github("compgenomr/compGenomRData")
Downloading GitHub repo compgenomr/compGenomRData@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/compgenomr/compGenomRData/tarball/HEAD' failed

Also tried githubinstall::githubinstall("compgenomr/compGenomRData") which did not work

2. Link: "https://github.com/compgenomr/exercises" leads to 404 error - no page under this address.

I would be very grateful if you could tell me how to solve these problems.

Yours sincerely

Gregor

Hi,
I successfully installed the package with the accompanying data and it worked well on my OS (Linux Manjaro).
Still, as it turns out that the uncompressed data are ~ 600MB large, installing git lfs (Git Large File Storage) before cloning the repository should help to avoid the error message caused by the download of the large files.

I would like to suggest adding these steps to the README:
Install git lfs: sudo apt-get install git-lfs (Debian-based Linux distros)
Set up git lfs: git lfs install

prior to the git clone/ devtools::install step.

Best,
Lorena