Unable to remove cells from Anndata matrix by an added .obs

Help
1

Hello,

Sorry if the title is not clear!

I have an anndata object:

adata
Out[10]: 
AnnData object with n_obs × n_vars = 13779 × 36601
    obs: 'doublet', 'doublet_score'
    var: 'gene_ids', 'feature_types'

I used DoubletDetection package to detect dublets in my reads matrix after creating the Anndata object immediately (before filtering or qc), and added the results to .obs like this:

import doubletdetection

clf = doubletdetection.BoostClassifier() 
doublets = clf.fit(adata.X).predict()
adata.obs['doublet'] = doublets
doublet_score = clf.doublet_score()
adata.obs['doublet_score'] = doublet_score

After detecting doublets it gives result as “0” for not a doublet and “1” for a doublet.

adata.obs['doublet'].value_counts()
Out[3]: 
0.0    12697
1.0     1074
Name: doublet, dtype: int64

What I want to do is remove all cells that have doublet value of “1” before continuing the rest of the analsysis, what I’ve tried to do is:

adata= adata[adata.obs["doublet"].isin[('0')],:]
or 
adata= adata[~adata.obs["doublet"].isin[('1')],:]

However, it does not remove doublets but either removes all cells or keep all cells

Out[38]: 
View of AnnData object with n_obs × n_vars = 0 × 36601
    obs: 'doublet', 'doublet_score'
    var: 'gene_ids', 'feature_types'

Out[42]: 
View of AnnData object with n_obs × n_vars = 13779 × 36601
    obs: 'doublet', 'doublet_score'
    var: 'gene_ids', 'feature_types'

How can I filter those cells? Is there a manual way like extracting the matrix with doublets data as a csv and deleting cells, then reading again?

Thanks in advance…

2

Have you checked the type of values in adata.obs.doublet? Currently you are filtering based on matching the string “0” or “1”, but you might need to do this with a regular integer 0/1.
I would do something like:
adata = adata[adata.obs[‘doublet’] == 0].copy()
I hope this helps!

3

Hi.

That worked!!! thank you very much.
Yes, I have been treating it as a string!
Thanks a lot.