Test alternative expression for all cell groups

Source code

Description

Test alternative expression for all cell groups

Usage

FindAllAltExp(
  object = NULL,
  assay = NULL,
  features = NULL,
  bind.name = "gene_name",
  bind.assay = NULL,
  bind.features = NULL,
  node = NULL,
  min.cells = 10,
  return.thresh = NULL,
  mode = c(1, 2, 3),
  test.use = c("DEXSeq", "PermTest"),
  threads = 0,
  perm = 100,
  seed = 999,
  pseudo.group = 3,
  debug = FALSE
)

Arguments

object A Seurat object.
assay Test assay (X). Default assay will be used if not set.
features Candidate list to test. If not set, will use AutoCorrFeatures(object, assay = assay).
bind.name Title name for binding features in the meta table. Consider most users start Yano to perform alternative splicing analysis, the default bind.name set to “gene_name”.
bind.assay Bind assay (Y). If not set, will aggregate all X values of the same block.
bind.features Candidate list for bind features to test. If not set, will test all covered.
node A node to find markers for and all its children; requires BuildClusterTree to have been run previously. Only can be used if test all groups.
min.cells Used to filter candiate features or binding features. Require them at least expressed in min.cells. Default is 10.
return.thresh Only return markers that have a p-value < return.thresh. Default is NULL.
mode Test mode. For mode 1, X (test feature) vs Y (binding feature). For mode 2, X vs (Y-X). For mode 3, X vs (Y+X).
threads Threads. For DEXSeq, threads will set to 1. For other methods, threads set to 0, which will auto check the CPU cores and set threads = number of CPU cores -1.
perm Permutation steps for calculate statistical of delta-ratio. Default is 100.
seed Seed for generate random number. Default is 999.
debug Print debug logs. Will auto set thread to 1. Default is FALSE.

Value

Data frame containing p values.

Examples

library("Yano")

data("glbt_small")
DefaultAssay(glbt_small) <- "exon"
alt.exon <- FindAllAltExp(object = glbt_small, bind.assay = "RNA", bind.name = "gene_name", features = rownames(glbt_small))
head(alt.exon)
data frame with 0 columns and 0 rows
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