defineControls: Definition of negative and positive control miRNAs for DANA...

In LXQin/DANA: Data-driven Normalization Assessment for miRNA-Seq Data

Definition of negative and positive control miRNAs for DANA normalization assessment

Description

Definition of negative and positive control miRNAs for DANA normalization assessment

Usage

defineControls(raw, tZero, tPoor, tWell, clusters)

Arguments

raw	Raw read count matrix (rows = genes, cols = samples). The matrix rows and columns must be named, with rownames=miRNAs and colnames=samples.
tZero	Lower (read count) bound for the definition of negative controls.
tPoor	Upper (read count) bound for the definition of negative controls.
tWell	Lower (read count) bound for the definition of positive controls.
clusters	Named Vector of clusters. Associates each miRNA in raw to a polycistronic cluster. Usually generated using the function defineClusters.

Value

List of two vectors:

posControls

Vector of positive control markers (miRNAs) in raw.

negControls

Vector of negative control markers (miRNAs) in raw.

LXQin/DANA documentation built on March 7, 2024, 3:24 a.m.