How to handle multiple fragment files for fragFilePath

[maggiebr0wn]

Hello! Thanks for making a cool shiny app concept for multiome data.

If there are multiple fragment files (for instance, I have over 30 samples), what do you suggest for the fragFilePath?

Thanks!

[aa20g217]

Hey,

Could you please verify the number of Fragment objects in your Seurat object using the following code?

DefaultAssay(pbmc) = "peaks"
frags <- Fragments(pbmc)
length(frags)  #should be equal to the number of your fragment files

To individually set the fragment file path for each fragment object, you can iterate through them and assign the file path. Ideally, the following code should work, but I could not test it due to data unavailability.

DefaultAssay(pbmc) = "peaks"
frags <- Fragments(pbmc)

# List of fragment file paths
fragFiles = c("file1", "file2", "..")

for (i in 1:length(frags)) {
  frags[[i]] <- UpdatePath(frags[[i]], new.path = fragFiles[i])
}

Fragments(pbmc) <- NULL
Fragments(pbmc) <- frags

Please let us know if the issue persists.