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Roy-lab / scMTNI

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Running method with single cluster #8

Closed PeterZZQ closed 6 months ago

PeterZZQ commented 1 year 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 1 year 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 1 year ago

Yes it works. Thank you!

PeterZZQ commented 1 year 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 1 year 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