estimateSizeFactorsForMatrix: Function to calculate the size factor for the single-cell...

In cole-trapnell-lab/monocle-release: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Function to calculate the size factor for the single-cell RNA-seq data

@importFrom stats median

Usage

estimateSizeFactorsForMatrix(counts, locfunc = median, round_exprs = TRUE,
  method = "mean-geometric-mean-total")

Arguments

counts	The matrix for the gene expression data, either read counts or FPKM values or transcript counts
locfunc	The location function used to find the representive value
round_exprs	A logic flag to determine whether or not the expression value should be rounded
method	A character to specify the size factor calculation appraoches. It can be either "mean-geometric-mean-total" (default), "weighted-median", "median-geometric-mean", "median", "mode", "geometric-mean-total".

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.