estimate_size_factors: Function to calculate size factors for single-cell RNA-seq...

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Function to calculate size factors for single-cell RNA-seq data

Description

Function to calculate size factors for single-cell RNA-seq data

Usage

estimate_size_factors(
  cds,
  round_exprs = TRUE,
  method = c("mean-geometric-mean-total", "mean-geometric-mean-log-total")
)

Arguments

cds	The cell_data_set
round_exprs	A logic flag to determine whether or not the expression value should be rounded
method	A string to specify the size factor calculation approach. Options are "mean-geometric-mean-total" (default), "mean-geometric-mean-log-total".

Value

Updated cell_data_set object with a new colData column called 'Size_Factor'.

Examples

  
    cds <- load_a549()
    colData(cds)[['Size_Factor']] <- NULL
    cds <- estimate_size_factors(cds)
  

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.