Skip to content

Conversation

@jamespeapen
Copy link
Member

Return a non transposed matrix since the transformTFIDF output currently need to be transposed again.

From the vignette (https://huishenlab.github.io/compartmap/articles/compartmap.html#running-the-compartmap-workflow):

# TF-IDF transform the signals
k562_scrna_chr14_tfidf <- transformTFIDF(assay(k562_scrna_se_chr14))

# Add back the TF-IDF counts to the object in the counts slot
assay(k562_scrna_se_chr14, "counts") <- t(k562_scrna_chr14_tfidf)

Are there any conditions where the function needs to return a transposed matrix?

it would need to be transposed again to put in the assay slot
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant