Opt_MeanSD_RTAM2: Optimizing Function in RTAM2

In alimahdipour/sciCNV: sciCNV

Optimizing Function in RTAM2

Description

An auxiliary fucntion to detect the optimal number of top-expressed genes for scaling a data-set using RTAM2

Usage

Opt_MeanSD_RTAM2(
  Normalized_log,
  Order_Matrix,
  G_mtrx,
  nGene,
  Min_nGene,
  gene_cutoff
)

Arguments

Normalized_log	the matrix of Log2(.+1)-normalized data
Order_Matrix	the matrix of original order of gene expressions per cell
G_mtrx	TPM-normalized matrix of the data
nGene	number of expressed genes
Min_nGene	minimum number of expressed genes across entire population
gene_cutoff	the cutoff to calculate the summation of top (nonzero) gene expressions

Value

The output is the CV (sd/mean) of RTAM2 normalization for given nGene, Min_nGene and gene_cutoff

Note

Please refer to the reference and supplemental materials described in the README for additional details.

Author(s)

Ali Mahdipour-Shirayeh, Princess Margaret Cancer Centre, University of Toronto

Examples

CV_for_RTAM2 <- Opt_MeanSD_RTAM2(Normalized_log=normalized_data, Order_Matrix, nGene, Min_nGene=250, gene_cutoff=250)

alimahdipour/sciCNV documentation built on Oct. 16, 2022, 12:56 p.m.