initialize_ploidy_group: Group-wise ploidy pre-initialization

In rujinwang/SCOPE: A normalization and copy number estimation method for single-cell DNA sequencing

Group-wise ploidy pre-initialization

Description

Pre-estimate ploidies across cells with shared clonal memberships

Usage

initialize_ploidy_group(Y, Yhat, ref, groups, 
                        maxPloidy = 6, minPloidy = 1.5,
                        minBinWidth = 5, SoS.plot = FALSE)

Arguments

Y	raw read depth matrix after quality control procedure
Yhat	normalized read depth matrix
ref	GRanges object after quality control procedure
groups	clonal membership labels for each cell
maxPloidy	maximum ploidy candidate. Defalut is 6
minPloidy	minimum ploidy candidate. Defalut is 1.5
minBinWidth	the minimum number of bins for a changed segment. Defalut is 5
SoS.plot	logical, whether to generate ploidy pre-estimation plots. Default is FALSE.

Value

ploidy.SoS

Vector of group-wise pre-estimated ploidies for each cell

Author(s)

Rujin Wang [e-mail]

Examples

Gini <- get_gini(Y_sim)

# first-pass 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

# Group-wise ploidy initialization
clones <- c("normal", "tumor1", "normal", "tumor1", "tumor1")
ploidy.sim.group <- initialize_ploidy_group(Y = Y_sim, Yhat = Yhat.noK.sim, 
                                ref = ref_sim, groups = clones)
ploidy.sim.group

rujinwang/SCOPE documentation built on Jan. 1, 2023, 5:40 a.m.