haystack: The main Haystack function

In singleCellHaystack: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

The main Haystack function

Description

The main Haystack function

Usage

haystack(x, ...)

## S3 method for class 'matrix'
haystack(
  x,
  expression,
  weights.advanced.Q = NULL,
  dir.randomization = NULL,
  scale = TRUE,
  grid.points = 100,
  grid.method = "centroid",
  ...
)

## S3 method for class 'data.frame'
haystack(
  x,
  expression,
  weights.advanced.Q = NULL,
  dir.randomization = NULL,
  scale = TRUE,
  grid.points = 100,
  grid.method = "centroid",
  ...
)

## S3 method for class 'Seurat'
haystack(
  x,
  coord,
  assay = "RNA",
  slot = "data",
  dims = NULL,
  cutoff = 1,
  method = NULL,
  weights.advanced.Q = NULL,
  ...
)

## S3 method for class 'SingleCellExperiment'
haystack(
  x,
  assay = "counts",
  coord = "TSNE",
  dims = NULL,
  cutoff = 1,
  method = NULL,
  weights.advanced.Q = NULL,
  ...
)

Arguments

x	a matrix or other object from which coordinates of cells can be extracted.
...	further parameters passed down to methods.
expression	a matrix with expression data of genes (rows) in cells (columns)
weights.advanced.Q	If NULL naive sampling is used. If a vector is given (of length = no. of cells) sampling is done according to the values in the vector.
dir.randomization	If NULL, no output is made about the random sampling step. If not NULL, files related to the randomizations are printed to this directory.
scale	Logical (default=TRUE) indicating whether input coordinates in x should be scaled to mean 0 and standard deviation 1.
grid.points	An integer specifying the number of centers (gridpoints) to be used for estimating the density distributions of cells. Default is set to 100.
grid.method	The method to decide grid points for estimating the density in the high-dimensional space. Should be "centroid" (default) or "seeding".
coord	name of coordinates slot for specific methods.
assay	name of assay data for Seurat method.
slot	name of slot for assay data for Seurat method.
dims	dimensions from coord to use. By default, all.
cutoff	cutoff for detection.
method	choose between highD (default) and 2D haystack.

Value

An object of class "haystack"

singleCellHaystack documentation built on Dec. 28, 2022, 1:29 a.m.