getx1.rnaseq: compute mixture data given projection matrix (RNAseq)

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

Description

compute mixture data given projection matrix (RNAseq)

Usage

getx1.rnaseq(
  NB0 = "top_bonferroni",
  resultb0,
  dge_s,
  MAXITER = 1000,
  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"
resultb0	output of getb0.rnaseq
dge_s	output of getdge
MAXITER	integer number of iterations allowed
x0	initial cell type composition for fitting

Value

x1 cell mixture of sample

converged convergence. 1=converged

Examples

## Not run: 
data("data_celltypes_rnaseq") 
dge.celltypes = getdge(cnts.celltypes, design.rnaseq, ncpm.min=1, nsamp.min=4)
b0 = getb0.rnaseq(dge.celltypes, design.rnaseq, ncpm.min=1, nsamp.min=4, sigg=NULL)
resultx1 = getx1.rnaseq(NB0="top_bonferroni",b0,dge.celltypes)

## End(Not run)

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