ScaleCounts: Normalize, adjust feature variance, and scale data matrix

In yanwu2014/swne: Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets

Normalize, adjust feature variance, and scale data matrix

Description

Normalize, adjust feature variance, and scale data matrix

Usage

ScaleCounts(
  counts,
  batch = NULL,
  method = "log",
  adj.var = T,
  plot.var.adj = F,
  gam.k = 10,
  scale.factor = NULL
)

Arguments

counts	Input data matrix
batch	Factor with batch identity for each sample
method	Scaling method
adj.var	Whether or not to apply mean variance adjustment for features
plot.var.adj	Whether or not to plot the mean variance relationship
gam.k	Number of additive models to use for variance modeling
scale.factor	Scale factor (defaults to median total counts)

Value

Normalized and scaled data matrix

yanwu2014/swne documentation built on Aug. 5, 2023, 4:42 a.m.