getx1.biseq: compute mixture data given projection matrix (bisulfite...

In rosedu1/deconvSeq: Cell Type Deconvolution for RNA Sequencing and Bisulfite Sequencing

Description

compute mixture data given projection matrix (bisulfite sequencing)

Usage

getx1.biseq(
  NB0 = "top_bonferroni",
  b0,
  methmat,
  sample.id,
  celltypes,
  MAXITER = 10000,
  x0 = NULL
)

Arguments

NB0	number of genes to be retained, ordered by f-stat p-value. Other options: "all" uses all genes, "top_bonferroni" uses genes with adjusted p-values <0.05 after bonferroni correction, "top_fdr" uses genes with adjusted p-values <0.05 after FDR correction. Default is "top-bonferroni"
b0	output of getb0.biseq
methmat	a matrix of counts with rows corresponding to methylation sites and columns. Columns are: chr start end strand coverage1 numCs1 numTs1 coverage2 numCs2 numTs2 ....
sample.id	vector of sample IDs
celltypes	vector of cell types
MAXITER	integer number of iterations allowed
x0	initial cell type composition for fitting

Value

x1 cell mixture of sample

converged convergence

Examples

## Not run: 
data("data_celltypes_rrbs") 
b0.rrbs = getb0.biseq(methmat, design.rrbs, sigg=NULL)
resultx1 = getx1.biseq(NB0="top_bonferroni",b0.rrbs,methmat,sample.id.rrbs,celltypes.rrbs)

## End(Not run)

rosedu1/deconvSeq documentation built on Aug. 19, 2020, 7:10 p.m.