computeSizeFactors: Compute a size factor for each sample

In YosefLab/ImpulseDE2: Differential expression analysis of longitudinal count data sets

Compute a size factor for each sample

Description

This function computes size factors for each sample in the dataset and expands them to a matrix of the size of the dataset. Size factors scale the negative binomial likelihood model of a gene to the sequencing depth of each sample. Note that size factors on bulk and single-cell data are computed differently: Median ratio of data to geometric mean for bul data and normalised relative sequencing depth for single-cell data.

Usage

computeSizeFactors(matCountDataProc)

Arguments

matCountDataProc

(matrix genes x samples) Read count data.

Value

vecSizeFactors (numeric vector number of samples) Model scaling factors for each sample which take sequencing depth into account (size factors).

Author(s)

David Sebastian Fischer

See Also

Called by computeNormConst.

YosefLab/ImpulseDE2 documentation built on Sept. 17, 2022, 2:45 a.m.