SCBN: Compute the normalization factor to identify difference...

In FocusPaka/SCBN: A statistical normalization method and differential expression analysis for RNA-seq data between different species

Compute the normalization factor to identify difference expression (DE) of genes between different species

Description

To normalize read counts and identify difference expression(DE) of orthologous genes between different species.

Usage

SCBN(orth_gene, hkind, a=0.05)

Arguments

orth_gene	Matrix or data.frame containing read counts and gene length for each orthologous gene between different species. The first and third column containing gene length, the second and the fourth column containing read counts.
hkind	A vector shows conserved genes position in orthologous genes.
a	P-value cutoff in iteration process to find the optimal normalization factor.

Value

list(.) A list of computed normalization factors, "median_val" represents foctors computed by median methods, "scbn_val" represents factors computed by SCBN methods.

Examples

data(sim_data)
SCBN(orth_gene=sim_data, hkind=1:1000, a=0.05)

FocusPaka/SCBN documentation built on April 20, 2023, 3:54 a.m.