Description Usage Arguments Value Author(s) Examples
A pdf file containing EM fitting results and plots is generated.
1 2  plot_EM_fit(Y_qc, gc_qc, norm_index, T, ploidyInt, beta0,
minCountQC = 20, filename)

Y_qc 
read depth matrix across all cells after quality control 
gc_qc 
vector of GC content for each bin after quality control 
norm_index 
indices of normal/diploid cells 
T 
a vector of integers indicating number of CNV groups.
Use BIC to select optimal number of CNV groups.
If 
ploidyInt 
a vector of initialized ploidy return from

beta0 
a vector of initialized binspecific biases returned from CODEX2 without latent factors 
minCountQC 
the minimum read coverage required for EM fitting.
Defalut is 
filename 
the name of output pdf file 
pdf file with EM fitting results and two plots: log likelihood, and BIC versus the number of CNV groups.
Rujin Wang rujin@email.unc.edu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21  Gini < get_gini(Y_sim)
# firstpass CODEX2 run with no latent factors
normObj.sim < normalize_codex2_ns_noK(Y_qc = Y_sim,
gc_qc = ref_sim$gc,
norm_index = which(Gini<=0.12))
Yhat.noK.sim < normObj.sim$Yhat
beta.hat.noK.sim < normObj.sim$beta.hat
fGC.hat.noK.sim < normObj.sim$fGC.hat
N.sim < normObj.sim$N
# Ploidy initialization
ploidy.sim < initialize_ploidy(Y = Y_sim,
Yhat = Yhat.noK.sim,
ref = ref_sim)
ploidy.sim
plot_EM_fit(Y_qc = Y_sim, gc_qc = ref_sim$gc,
norm_index = which(Gini<=0.12), T = 1:7,
ploidyInt = ploidy.sim,
beta0 = beta.hat.noK.sim,
filename = 'plot_EM_fit_demo.pdf')

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