Error running differential comparison

cresswellkg commented 5 years ago

I've been trying to run differential TAD comparison using the sample data provided. The code I use is:

RHiCDB(list('h1_rep1','h1_rep1'),10000,'hg19',ref='hg19');

This is identical to the sample code on Github but I get the following error:

Your input matrix is raw matrix, perform KR normalization find local maximum Error in tadscores[1:Ns, 1] : incorrect number of dimensions In addition: Warning message: In tmp[oridx] <- tadscores : number of items to replace is not a multiple of replacement length

caokai001 commented 4 years ago

Hi! cresswellkg What version of R are you using. I encountered an error. like this.

> install.packages("RHiCDB-master.zip")
Warning message:
package ‘RHiCDB-master.zip’ is not available (for R version 3.6.1)

Hope to receive your reply. Thanks!

ChenFengling commented 4 years ago

Hi! cresswellkg What version of R are you using. I encountered an error. like this.
> install.packages("RHiCDB-master.zip")
Warning message:
package ‘RHiCDB-master.zip’ is not available (for R version 3.6.1)
Hope to receive your reply. Thanks!

Can you install this package using devtools?

devtools::install_github("ChenFengling/RHiCDB")

caokai001 commented 4 years ago

Hello, thank you for your reply~ The server cannot link to github, so I download the offline package (RHiCDB-master.zip) and install it.

> devtools::install_github("ChenFengling/RHiCDB")
错误: Failed to install 'unknown package' from GitHub:
  Failed to connect to api.github.com port 443: 拒绝连接

caokai001 commented 4 years ago

Thanks! I have installed this package. 谢谢 @ChenFengling

caokai001 commented 4 years ago

Hi @ChenFengling ! I also want to detect the differential TAD between two hic sample. so I try this command.

RHiCDB(list('h1_rep1','h1_rep1'),10000,'hg19',ref='hg19');
[1] "differential CDB called by intersection!"
[1] "A. Processing the first sample  h1_rep1/"
[1] "* Detect all local maximum peaks on each chromosome."
[1] "Processing chr1"
Your input matrix is raw matrix, perform KR normalization
find local maximum
[1] "Processing chr2"
Your input matrix is raw matrix, perform KR normalization
find local maximum
[1] "Processing chr3"
Your input matrix is raw matrix, perform KR normalization
find local maximum
...
...
[1] "Processing chr22"
Your input matrix is raw matrix, perform KR normalization
find local maximum
[1] "Processing chr23"
Your input matrix is raw matrix, perform KR normalization
find local maximum
[1] " "
[1] "* Write outputs: localmax1.txt, allaRI1.txt, allLRI1.txt"
Error in file(file, ifelse(append, "a", "w")) : 'description'参数不对
此外: Warning message:
In if (file == "") file <- stdout() else if (is.character(file)) { :
  条件的长度大于一，因此只能用其第一元素

What do you think might have caused this result?

Hope to receive your reply. Thanks!

ChenFengling / RHiCDB

Error running differential comparison #2