estimateSizeFactorsForMatrix {monocle}R Documentation

Function to calculate the size factor for the single-cell RNA-seq data @importFrom stats median

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".


[Package monocle version 2.18.0 Index]