SMIXnorm: Produce SMIXnorm normalized expression matrix

In S-YIN/RSEQNORM: FFPE RNA-Seq Normalization

Description

Calls the SMIXnorm.mle function to obtain MLE of the simplified mixture model, then produces the normalized expression matrix.

Usage

SMIXnorm(dat, max_iter = 20, tol = 0.01, appr = T)

Arguments

dat	input raw read count matrix. dim of dat = J genes * I samples.
max_iter	maximum number of iterations for the nested EM algorithm default is 20, recommend range (10, 50).
tol	convergency criteria, default is 1e-2, recommend range (1e-5,1).
appr	binary True of False, indicates if the approximate version of normalization should be used.

Value

A list contains the normalized expression matrix (MIX_normalized_log), proportion of expressed genes (phi) and probabilities of being expressed for all genes (D).

S-YIN/RSEQNORM documentation built on March 8, 2020, 11:16 p.m.