normalize_codex2_ns_noK: Normalization of read depth without latent factors under the...

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

Normalization of read depth without latent factors under the case-control setting

Description

Assuming that all reads are from diploid regions, fit a Poisson generalized linear model to normalize the raw read depth data from single-cell DNA sequencing, without latent factors under the case-control setting.

Usage

normalize_codex2_ns_noK(Y_qc, gc_qc, norm_index)

Arguments

Y_qc	read depth matrix after quality control
gc_qc	vector of GC content for each bin after quality control
norm_index	indices of normal/diploid cells

Value

A list with components

Yhat	A list of normalized read depth matrix
fGC.hat	A list of estimated GC content bias matrix
beta.hat	A list of estimated bin-specific bias vector
N	A vector of cell-specific library size factor, which is computed from the genome-wide read depth data

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))

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