DiffGenes: Different expression with spatial single

In YeehanXiao/STREAM: STREAM: Spatial Transcriptomics data Analyses and Modeling

Different expression with spatial single

Description

Different expression with spatial single

Usage

DiffGenes(object, ...)

## S4 method for signature 'SPARK'
DiffGenes(object, numCores = 4, verbose = FALSE, ...)

## S4 method for signature 'giotto'
DiffGenes(
  object,
  minimum.k = 2,
  maximum.distance.delaunay = 400,
  bin.method = c("kmeans", "rank"),
  expression.value = "normalized",
  numCores = 5,
  verbose = TRUE,
  python_Path = NULL,
  ...
)

Arguments

object	a giotto object
...	Other graguments in spark.vc spark.test
numCores	The number of cores to use, 5 as default.
verbose	verbosity of the function
minimum.k	minimum nearest neigbhours if maximum_distance != NULL, default, 2.
maximum.distance.delaunay	distance cutoff for nearest neighbors to consider for Delaunay network, default 400
bin.method	method to binarize gene expression. Set k-means as default.
expression.value	expression values to use, choice with normalized, scaled and custom, default is normalized.
python_Path	python path. Path in Giotto object will be used when no extra dir is provided.

Value

Different expression data.fame

A list contain 4 methods of differentin expression

YeehanXiao/STREAM documentation built on Aug. 13, 2022, 6:43 p.m.