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Roy-lab / scMTNI

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Running method with single cluster #8

Closed PeterZZQ closed 2 months ago

PeterZZQ commented 12 months ago

Hello,

I wish to run the method with only one cluster in the dataset, may I know how I can set the celltype_tree_ancestor.txt. I tried to left the file empty, but it shows the error: 

Segmentation fault (core dumped)
shiluzhang commented 12 months ago

Hi Peter,

Thanks for trying scMTNI! celltype_tree_ancestor.txt file is not needed if there is only one cluster.

In step 3, we add the example command for running one cell cluster with prior or without prior: https://github.com/Roy-lab/scMTNI#example-usage-of-indep-with-prior-network-indep-single-cell-cluster-version-of-scmtni Code/scMTNI -f ExampleData/cluster1_config.txt -x50 -l ExampleData/cluster1_TFs_OGs.txt -n ExampleData/cluster1_AllGenes.txt -m ExampleData/cluster1_ogids.txt -s ExampleData/cluster1.txt -i yes -c yes -b -0.9 -q 0

https://github.com/Roy-lab/scMTNI#example-usage-of-indep-without-prior-network-indep-single-cell-cluster-version-of-scmtni Code/scMTNI -f ExampleData/cluster1_config_noprior.txt -x50 -l ExampleData/cluster1_TFs_OGs.txt -n ExampleData/cluster1_AllGenes.txt -m ExampleData/cluster1_ogids.txt -s ExampleData/cluster1.txt -i yes -c yes -b -0.9 -q 0

Please let me know if it still doesn't work.

Shilu

PeterZZQ commented 12 months ago

Yes it works. Thank you!

PeterZZQ commented 11 months ago

Hi, when running scMTNI with prior network, should the -q be 2 instead of 0 (see the first command above and in the README file)? I try the command above and found that the result is not affected by the prior network anymore.

shiluzhang commented 11 months ago

Hi Peter, Yes, good catch. -q should be set to non-zero for running scMTNI/INDEP with a prior network. You could try q={2,3,4}, a higher value of q will result in prior networks being valued more strongly to select an edge. I have updated the first command in the README file with Code/scMTNI -f ExampleData/cluster1_config.txt -x50 -l ExampleData/cluster1_TFs_OGs.txt -n ExampleData/cluster1_AllGenes.txt -m ExampleData/cluster1_ogids.txt -s ExampleData/cluster1.txt -i yes -c yes -b -0.9 -q 2. Thanks!

Best, Shilu