SuvojitHazra
commented
10 months ago Re: Generating celltype_tree_ancestor.txt file
Thanks for your interest in scMTNI. You may generate the celltype_tree_ancestor.txt now by following inputs here:
Point-1. First, you make an empty text file named celltype_tree_ancestor.txt in text editor (e.g., Vi for Linux, Notepad++ for Windows). Remember the celltype_tree_ancestor.txt text file will have four tab-separated columns: • Leftmost column: Child cell/node. Default value in string/name. • Second leftmost column: Parent cell/node. Default value in string/name. • Second rightmost column: Branch-specific gain rate (The probability that an edge is gained in a child given that the edge is absent in the predecessor cell). The default floating value is 0.2. • Rightmost column: Branch-specific loss rate (The probability that an edge is lost in a child given that the edge is present in the predecessor cell). The default floating value is 0.2.
Point-2. Check the Figure attached. The figure consists of a cell fate transition lineage tree of three types of cells, namely, Celltype1, Celltype2 and Celltype3. Theoretically, the tree contains two ancestral parent nodes, namely, Predecessor cell 1 and Predecessor cell 2 in cell-state lineage (see, attached Figure). Therefore, the tree connections between the three extant cell-types (Celltype1, Celltype2 and Celltype3) can be made using these two parent nodes. Using Point-1, the celltype_tree_ancestor.txt is made as depicted in attached Figure.
Please cite this if you use scMTNI: Zhang, S., Pyne, S., Pietrzak, S., Halberg, S., McCalla, S.G., Siahpirani, A.F., Sridharan, R. and Roy, S., Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Nat Commun 14, 3064 (2023). https://doi.org/10.1038/s41467-023-38637-9
How can i generate celltype_tree_ancestor.txt file? Thanks