integrate.by.avg: integrate dataset by calculating the average expression and...

In Japrin/sscClust: simpler single cell RNAseq data clustering

integrate dataset by calculating the average expression and then clustering the pseudo bulk data

Description

integrate dataset by calculating the average expression and then clustering the pseudo bulk data

Usage

integrate.by.avg(
  sce.list,
  out.prefix,
  assay.name = "exprs",
  is.avg = FALSE,
  ncores = 6,
  use.deg = TRUE,
  gene.de.list = NULL,
  sort.by = "F.rank.median",
  avg.by = "majorCluster",
  n.downsample = NULL,
  n.pc = 15,
  do.clustering = T,
  de.stat = "t",
  de.thres = 1,
  do.scale = F,
  par.clust = list(method = "SNN", SNN.k = 3, SNN.method = "leiden",
    resolution_parameter = 2.2),
  topGene.lo = -1.5,
  topGene.hi = 1.5,
  topGene.step = 1,
  myseed = 9997,
  verbose = F,
  method.avg = "zscore",
  ...
)

Arguments

sce.list	list; list of object of singleCellExperiment class
out.prefix	character; output prefix.
assay.name	character; which assay (default: "exprs")
is.avg	logical; whether the objects in sce.list are average expression (default: FALSE)
ncores	integer; number of cores to use (default: 6)
use.deg	logical; whether use only the differentially expressed genes (default: FALSE)
gene.de.list	list; if not NULL, each element is a data.frame with "geneID" column (default: NULL)
sort.by	character; by which to sort genes and the top ones will be used for clustering. One of "F.rank.median", and "occurence" (default: "F.rank.median")
avg.by	character; calculate the average expression of cells group by the specifid column (default: "majorCluster")
n.downsample	integer; number of cells in each cluster to downsample to (default: NULL)
n.pc	integer; number of pc ot use (default: 15)
do.clustering	logical; wheter perform PCA/clustering (default: TRUE)
de.stat	character; column in gene.de.file (default: "t")
de.thres	double; used for selecting genes. can be larger than 1(top number of genes) or less than 1 (F.rank threshold) (default: 2000)
do.scale	logical; scale the summarized vectors (default: false)
par.clust	list; parameters for clustering method (default: list(method="SNN",SNN.k=3,SNN.method="leiden",resolution_parameter=2.2))
topGene.lo	double; for top gene heatmap.(default: -1.5)
topGene.hi	double; for top gene heatmap.(default: 1.5)
topGene.step	double; for top gene heatmap.(default: 1)
myseed	integer; seed for random number generation.(default: 9997)
verbose	logical; verbose level.(default: FALSE)
method.avg	character; method of calculate the average expression. Passed to 'avg' of 'ssc.average.cell'.(default: "zscore")
...	parameters passed to ssc.clusterMarkerGene

Details

method to calculate the average expression can be one of "mean", "zscore"

Japrin/sscClust documentation built on Dec. 15, 2022, 1:04 p.m.