View source: R/expression_distance.R
estimateExpressionChange | R Documentation |
Expression shift magnitudes per cluster between conditions
estimateExpressionChange(
cm.per.type,
sample.groups,
cell.groups,
sample.per.cell,
dist = NULL,
dist.type = c("shift", "total", "var"),
verbose = FALSE,
ref.level = NULL,
n.permutations = 1000,
p.adjust.method = "BH",
top.n.genes = NULL,
gene.selection = "wilcox",
n.pcs = NULL,
trim = 0.2,
n.cores = 1,
...
)
cm.per.type |
List of normalized count matrices per cell type |
sample.groups |
Named factor with cell names indicating condition/sample, e.g., ctrl/disease |
cell.groups |
Named clustering/annotation factor with cell names |
dist |
what distance measure to use: 'JS' - Jensen-Shannon divergence (default), 'cor' - Pearson's linear correlation on log transformed values |
verbose |
(default=FALSE) |
n.cores |
number of cores (default=1) |
List of distances per cell type, distance matrices, sample groups, cell types, pvalues, and adjusted p-values.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.