batch

[b1lake]

Hi, when including a batch factor when creating a new pagoda2 object I am now getting the following error:

p2 <- Pagoda2$new(x = countMatrix, trim=10, batch = countMatrix.batch) Error in initialize(...) : unused argument (batch = countMatrix.batch)

Any way to rectify this?

Thanks!

Blue

[evanbiederstedt]

Hi @b1lake

Thanks for the issue.

This is interesting! It didn't occur to me previously that users would initialize Pagoda2 objects with the batch param.

~Currently, the following code should work:~

p2 <- Pagoda2$new(x = countMatrix, trim=10)
p2$batch <- countMatrix.batch

~Given you say you are now receiving this error, I'm happy to revert to the behavior whereby you can do:~

p2 <- Pagoda2$new(x = countMatrix, trim=10, batch = countMatrix.batch)

Update: Hi @b1lake I actually think this is a bug based on how I converted the R6 code. I didn't notice this previously. I'll fix shortly.

[evanbiederstedt]

Hello @b1lake

I think the issue is now fixed---this is my error; I didn't notice that people would set batch via the Pagoda2 constructor. Thanks for pointing this out :)

Try installing pagoda2 via the following:

git clone https://github.com/kharchenkolab/pagoda2.git
cd pagoda2
git checkout devel
git pull origin devel --force
R CMD BUILD .
R CMD INSTALL *gz

Then this should work:

p2 <- Pagoda2$new(x = countMatrix, trim=10, batch = countMatrix.batch)

Please let me know. If it works, we'll push to the main branch. There are several updates to make since publishing on CRAN.

Thanks, Evan

[evanbiederstedt]

Fix should be on the main branch now as well

[b1lake]

Great! This works, thank you for fixing this so quickly!

[evanbiederstedt]

That's great to hear! Thanks again

Best, Evan