calculateCQN: Normalize read counts matrix using the cqn method.

In kauralasoo/seqUtils:

Description

Quantile normalize read counts while correcting for feature length and GC countent.

Usage

calculateCQN(counts_matrix, gene_metadata, return_type = "normalised")

Arguments

counts_matrix	Matrix of read counts.
gene_metadata	data.frame with at least three columns: gene_id, percentage_gc_content and length.
return_type	If return_type == "normalised" then return normalized expression matrix, otherwise return cqn object.

Value

Quantile-normalized and GC-corrected matrix.

Author(s)

Kaur Alasoo

kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.