hippo_diffexp: HIPPO's differential expression

Description Usage Arguments Value Examples

View source: R/hippo.R

Description

HIPPO's differential expression

Usage

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hippo_diffexp(
  sce,
  top.n = 5,
  switch_to_hgnc = FALSE,
  ref = NA,
  k = NA,
  plottitle = ""
)

Arguments

sce

SingleCellExperiment object with hippo

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

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data(toydata)
set.seed(20200321)
toydata = hippo(toydata,K = 10,z_threshold = 1,outlier_proportion = 0.01)
result = hippo_diffexp(toydata)

HIPPO documentation built on Nov. 8, 2020, 5:05 p.m.