calculate_clr: Calculate CLR

In warrenmcg/sleuth-ALR: Compositional Approach to Sleuth Data Analysis

Description

This function calculates the centered logratio transformation (subtracting geometric mean of all features within each sample).

Usage

calculate_clr(mat, base = "e", denom_method = "geomean")

Arguments

mat	an D x M matrix of D target IDs and M samples
base	what should the base of the logarithm be? currently only supports base "e" and base 2.
denom_method	either 'geomean' or 'DESeq2' to use either the geometric mean of all features as the denominator, or the DESeq2-style size factors as the denominator (equivalent to using standard DESeq2-style normalization, which is used in standard sleuth)

Value

D x M matrix of CLR-transformed values, centered on the geometric mean of all features within each sample

warrenmcg/sleuth-ALR documentation built on Oct. 27, 2020, 4:30 a.m.