hippo_diffexp: HIPPO's differential expression

In tk382/HIPPO: Heterogeneity-Induced Pre-Processing tOol

Description

HIPPO's differential expression

Usage

hippo_diffexp(
  sce,
  method = "pois",
  top.n = 15,
  switch_to_hgnc = FALSE,
  ref = NA,
  k = NA,
  plottitle = ""
)

Arguments

sce	SingleCellExperiment object with hippo
method	whether to use Poisson likelihood test vs Gaussian different mean test
top.n	number of markers to return
switch_to_hgnc	if the current gene names are ensemble ids, and would like to switch to hgnc
ref	a data frame with columns 'hgnc' and 'ensg' to match each other, only required when switch_to_hgnc is set to TRUE
k	number of rounds of clustering that you'd like to see result. Default is 1 to K
plottitle	title of the resulting plot

Value

list of differential expression result

Examples

data(toydata)
set.seed(20200505)
toydata = hippo(toydata,
          feature_method = "zero_inflation",
          clustering_method = "kmeans",
          K = 4,
          outlier_proportion = 0.00001)
result = hippo_diffexp(toydata, method = "gaus")

tk382/HIPPO documentation built on Aug. 17, 2021, 2:29 p.m.