Man pages for elkebir-group/phydoser
Design a follow-up single-cell sequencing experiment from bulk sequencing data
| AML38 | phydose tutorial dataset of a patient (AML-38) with acute... |
| AML38DFF | AML38 corresponding distinguishing feature families |
| CalcU | Generates the clonal prevalence matrix U by mutlplying the... |
| CreateDOT | Convert a binary tree to dot format |
| dot-CleanFmatrix | Cleans the raw dataframe frequency matrix and converts it... |
| dot-CreateF | Creates an F matrix from character vector |
| dot-CreateGraphDot | Create a tree in dot format |
| dot-CreateKey | Create a key that maps the columns of the trees and... |
| dot-CreateParentList | Creates a list of of the parents for each node |
| dot-CreateTree | Creates a binary matrix tree with clones as rows and... |
| dot-GetAllF | Converts all frequency matrices in the character vector to a... |
| dot-GetAllTrees | Helper function to read in all trees from a file and convert... |
| dot-SortMat | sort a matrix that represents a tree |
| generateDistFeat | Generate the distinguishing feature family for a set of trees |
| phydata | phydose example dataset of two trees |
| phydataDFF | phydose example distinguishing feature families |
| phydose | Determine the number of cells to sequence in a follow-up... |
| phydose-package | A short title line describing what the package does |
| plotTree | Plot a tree in the set |
| rcpp_hello_world | Simple function using Rcpp |
| ReadJoint | Read a file containing a candidate set of trees and an... |
| ReadJointDir | Read in data from a directory |
| ReadTrees | Read in set of candidate trees in the given directory and... |
| Reconcile | Calculate the support for each distinguishing feature in a... |
| solveFLower | Find the frequencies to use for the k star confidence... |
| solveFUpper | Find the frequencies to use for the k star confidence... |
