deva_normalization: Normalization of data to prepare for deva. Uses a Median of...
In ruggleslab/blacksheepr: Outlier Analysis for pairwise differential comparison

View source: R/outlier_analysis_functions.R

deva_normalization

R Documentation

Normalization of data to prepare for deva. Uses a Median of Ratio method followed by a log2 transformation.

Description

Normalization of data to prepare for deva. Uses a Median of Ratio method followed by a log2 transformation.

Usage

deva_normalization(intable, method = "MoR-log")

Arguments

`intable`	table with samples along the columns and features along the rows.
`method`	DEFAULT: "MoR-log"; Method by which to normalize data in preparation for deva. Options are <"MoR-log", "MoR", "log">. Where "MoR" refers to the Median of ratio's. The "log" transformation is necessary to compress heavily skewed data and allow for proper detection. "MoR-log" as the default will perform MoR followed by a log2 transform.

Value

A normalized table for input into deva

Examples

library(pasilla)
pasCts <- system.file("extdata",
    "pasilla_gene_counts.tsv", package="pasilla")
cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
norm_cts <- deva_normalization(cts, method = "MoR-log")

ruggleslab/blacksheepr documentation built on Feb. 27, 2023, 10:40 p.m.