func_SMIXnorm: Produce SMIXnorm normalized expression matrix

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

Description

This function calls the SMIXnorm function to obtain MLE of the mixture model, then produces the normalized expression matrix.

Usage

func_SMIXnorm(
  dat,
  max_iter = 15,
  tol = 0.01,
  log_file = "SMIXnorm.log",
  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 15, recommend range (10, 50).
tol	convergency criteria, default is 1e-2, recommend range (1e-5,1).
log_file	file name that records the log. Default log file name is SMIXnorm.log.
appr	binary True of False, indicates if the approximate version of normalization should be used.

Value

A list contains the normalized expression matrix, proportion of expressed genes and probabilities of being expressed for all genes.

S-YIN/FFPEnorm documentation built on Nov. 20, 2019, 7:05 a.m.