Issue with Downloading Precalculated Parameters in scan Function

[RemagenRe]

Dear DiffScan Development Team,

I hope this message finds you well. I am encountering an issue when using the scan function from the DiffScan package. Specifically, the function attempts to download precalculated parameters from OneDrive but times out. I manually downloaded the required file, "Qmax_null.rds," from another source, but I'm unsure how to properly load it into the environment for the scan function to use.

Here is the relevant section of my code and output:

> library(DiffScan)

> library(dplyr)

> set.seed(123)

> r = list(
+   t1 = tibble(A1 = runif(50), A2 = A1 + runif(50, -0.1, 0.1),
+               B1 = A1 + runif(50, -0.1, 0.1), B2 = B1 + runif(50, -0.1,  .... [TRUNCATED] 

> r_init = init(r, qc_ctrl = F, ncores = 1)
2 rnas in total
skip quality control

> r_norm = normalize(r_init, ncores = 1)
merge transcripts
normalize to [0,1]
quantile normalization
meanA:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.2425  0.4567  0.4987  0.7843  1.0000 
meanB:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.2343  0.5134  0.5161  0.8234  0.9980 
determine invariant set
    max_cor     len_inv    prop_inv    lower_qt    upper_qt prop_inv_ss prop_inv_ds 
  0.9240215 115.0000000   0.5750000   0.4000000   0.6500000   0.4400000   0.5600000 
fit rlm
transform
traceback

> options(timeout = 300)

> Qmax_null <- readRDS("Qmax_null.rds")

> assign("Qmax_null", Qmax_null, envir = .GlobalEnv)

> res = scan(r_norm$r, seed = 123, alpha = 0.05, ncores = 1)
First time to run scan. Downloading precalculated parameters ...
trying URL 'https://onedrive.live.com/download?resid=3D9C2C35D99F543F%2134216&authkey=!AH2XMY2d6FUe0mo&download=1'
Error in download.file(url = "https://onedrive.live.com/download?resid=3D9C2C35D99F543F%2134216&authkey=!AH2XMY2d6FUe0mo&download=1",  : 
  cannot open URL 'https://onedrive.live.com/download?resid=3D9C2C35D99F543F%2134216&authkey=!AH2XMY2d6FUe0mo&download=1'
In addition: Warning message:
In download.file(url = "https://onedrive.live.com/download?resid=3D9C2C35D99F543F%2134216&authkey=!AH2XMY2d6FUe0mo&download=1",  :
  URL 'https://onedrive.live.com/download?resid=3D9C2C35D99F543F%2134216&authkey=!AH2XMY2d6FUe0mo&download=1': Timeout of 300 seconds was reached
> 

I would greatly appreciate any guidance on how to correctly load the precalculated "Qmax_null.rds" file into the scan function without triggering the download attempt.

Thank you for your time and assistance!

[yub-hutch]

Hi,

The download process works well on my end. Can you directly access the download link in your browser?

To avoid the download, you can copy Qmax_null.rds to file.path(find.package('DiffScan'), '/R/Qmax_null.rds').

Thanks, Bo

[RemagenRe]

Hi,

The download process works well on my end. Can you directly access the download link in your browser?

To avoid the download, you can copy Qmax_null.rds to file.path(find.package('DiffScan'), '/R/Qmax_null.rds').

Thanks, Bo

Thank you for your prompt assistance regarding the Qmax_null.rds file. Your suggestion worked perfectly, and I was able to proceed without issues. I genuinely appreciate your support.

However, I have encountered another problem. The link to the scripts and data on DiffScan GitHub homepage (https://cloud.tsinghua.edu.cn/published/diffscan_scripts_and_data) appears to be inactive. I was hoping to access the materials for reproducing the analyses and results mentioned in the DiffScan paper.

Could you provide an alternative link or make the content available through another platform?

Thank you once again for your help.