findBestK: Testing multiple K for RUV4 batch correction to find the best...

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Testing multiple K for RUV4 batch correction to find the best K.

Description

Testing multiple K for RUV4 batch correction to find the best K.

Usage

findBestK(
  spe,
  maxK = 10,
  factor_of_int,
  factor_batch,
  NCGs,
  point_size = 3,
  line_col = "black",
  point_col = "black",
  text_size = 13
)

Arguments

spe	A Spatial Experiment object.
maxK	Integer. The max k to test, will test k from 1 to maxK, by default is 10.
factor_of_int	Column name(s) to indicate the factors of interest. This is required for the RUV4 method.
factor_batch	Column name to indicate the batch.
NCGs	Negative control genes. This is required for the RUV4 method.
point_size	Numeric. Plotting parameter.
line_col	Character. Plotting parameter.
point_col	Character. Plotting parameter.
text_size	Numeric. Plotting parameter.

Value

A ggplot object.

Examples

data("dkd_spe_subset")
spe <- findNCGs(dkd_spe_subset, top_n = 100)
findBestK(spe,
  factor_of_int = c("disease_status"),
  factor_batch = "SlideName", NCGs = S4Vectors::metadata(spe)$NCGs
)

DavisLaboratory/standR documentation built on March 28, 2024, 4:23 a.m.