phydose: Determine the number of cells to sequence in a follow-up...

In elkebir-group/phydoser: Design a follow-up single-cell sequencing experiment from bulk sequencing data

Description

Determine the number of cells to sequence in a follow-up single cell experiment

Usage

phydose(
  trees,
  fmatrices = NULL,
  umatrices = NULL,
  distFeat = NULL,
  gamma = 0.95,
  fnr = 0,
  kstar_quant = 1
)

Arguments

trees	a list of binary matrices representing trees with clones as the rows and mutations as the columns
distFeat	a optional list of distinguishing features in the same order as the trees
gamma	a number that determines the confidence level of the users of observing the tree during sequencing, defaults to 0.95
fnr	a number between 0 and 1 that represents the false negative rate of the sequencing technology, defaults to 0
kstar_quant	the quantile that determines
fmatries	a list of frequency matrices with samples as the rows and mutation frequencies (VAFs) as the columns

Value

a list that contains the value of k* and a dataframe that contains the value of k for for each tree and sample

Examples

phydose(trees = phydata$trees, fmatrices = phydata$fmatrices)
phydose(trees = phydata$trees umatrices = phdata$u_list)
## Not run: 
phydose(trees = AML38$trees, fmatrices = AML38$fmatrices, fnr= 0.05)

## End(Not run)

elkebir-group/phydoser documentation built on July 16, 2020, 4:43 p.m.