analyze_clustering: This function analyzes ST data based on clustering generated...
In tmirus/TTT: What the Package Does (One Line, Title Case)

This function analyzes ST data based on clustering generated by cluster_counts_OL. It calculates a list of genes specific to a certain cluster and identifies differentually expressed genes across clusters

analyze_clustering(
  counts,
  ids,
  clustering,
  sig.level = 0.001,
  lasso.data = NULL,
  deg.weight = 2,
  lls.weight = 3,
  entropy.weight = 1,
  build.lasso = FALSE,
  gamma = 3,
  ncores = 4,
  normalize = FALSE,
  verbose = TRUE
)

`counts`	non-negative numeric matrix containing gene counts, rows correspond to spots, columns correspond to genes
`ids`	data frame or matrix assigning spatial coordinates to the spots (see process_input() for details)
`clustering`	list containing clustering information as returned by cluster_counts_OL (numeric vector assigning spots to clusters)
`sig.level`	significance level for the t-test between clusters; genes with p-values above this threshold will be removed from output; default 0.05
`lasso.data`	output of build_lassos function
`deg.weight`	numeric, weight of the ranking of genes by differential gene expression in the overall ranking; default 2
`lls.weight`	numeric, weight of the ranking of genes by lls fit in the overall ranking; default 3
`build.lasso`	logical, should lasso models be calculated? only used if lasso.data is NULL, default FALSE
`gamma`	numeric, gamma value passed to build_lassos. Determines ration of sparsity and smoothness in the model, default 3
`ncores`	integer, number of cores used for lasso calculation; default 4
`normalize`	logical, should counts be normalized with sctransform prior to differential expression testing? default FALSE
`verbose`	logical, default TRUE
`entropy.weightnumeric,`	weight of the ranking of genes by entropy in the overall ranking; default 1

list with 2 entries:

differential genes - data frame containing information (name, ckuster, p-value, up-/downregulation) for differentially expressed genes. Ordered by gene rank.
gene.cluster.table - data frame containing for each gene in differential.genes the p-value for differential expression in each cluster

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.