deseq_size_factors: Get DESeq2 Size Factors
In warrenmcg/sleuth-ALR: Compositional Approach to Sleuth Data Analysis

Description Usage Arguments Value References

Function to return the DESeq2-style size factors of a collection of features. The geometric mean is calculated for feature across samples. Then the ratio of every sample observation to the geometric mean across samples is calculated. From there, the median of ratios within each sample is selected as the size factor.

1	deseq_size_factors(x, denoms = NULL)

`x`	a D x M matrix with D features (the denominator features) and M samples
`denoms`	a vector of either indices or feature names that match row names of the matrix. These are the ones that will be used for calculating the compositional normalization using the DESeq2-method.

a vector of the size factors for each sample

For a discussion of why the DESeq2 size factor is compatible with Compositional Normalization, see https://dx.doi.org/10.1093/bioinformatics/bty175

For the original DESeq2 method, see estimateSizeFactorsForMatrix

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