Description Usage Arguments Value Examples
This function is the first function to start calculate the subtree from dgeA, dgeB. This basically do the clustering and fullplot at low resolution
1 2 | Tree.build.prepare(dge1, dge2, name1, name2, first.reso = c(0.03, 0.03),
treemake.dir = "./")
|
dge1 |
the dge file (usually from earlier timepoint), either raw or processed is acceptable |
dge2 |
the dge file (usually from later timepoint), either raw or processed is acceptable |
name1 |
The name for the dge1 (usually from earlier timepoint) |
name2 |
The name for the dge2 (usually from later timepoint) |
first.reso |
The cluster resolution for dge1 and dge2 respectively. A vector of two number , for example c(0.03,0.03) |
treemake.dir |
A path. The workspace where the whole tree making project is on |
A list of stuff including seurat clutsering result; fullplots; the resolution used and the path
1 | S4_S5ROCK.tree.prep<-Tree.build.prepare(dge1=s4.B.dge,dge2=S5.ROCKII.dge,name1="S4.B",name2="S5.rock",first.reso=c(0.03,0.03),treemake.dir="/mnt/NFS/homeGene/JinLab/cxw486/Dropseq/Entrance/Esderived/Esdrived_DGE/AttemptFrom17.8.28/ROCKII/Treemake/")
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