Description Usage Arguments Value Examples
compute mixture data given projection matrix (bisulfite sequencing)
1 2 3 4 5 6 7 8 9 | getx1.biseq(
NB0 = "top_bonferroni",
b0,
methmat,
sample.id,
celltypes,
MAXITER = 10000,
x0 = NULL
)
|
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 |
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 |
x1 cell mixture of sample
converged convergence
1 2 3 4 5 6 | ## 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)
|
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