swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 656fc8b562d53e5d0cedda9e09d9dda81e8c00e9 authored by David Collins on 29 February 2024, 13:44:33 UTC
Merge pull request #8550 from satijalab/develop
Merge pull request #8550 from satijalab/develop
Tip revision: 656fc8b
RunSLSI.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/generics.R, R/dimensional_reduction.R
\name{RunSLSI}
\alias{RunSLSI}
\alias{RunSLSI.default}
\alias{RunSLSI.Assay}
\alias{RunSLSI.Seurat}
\title{Run Supervised Latent Semantic Indexing}
\usage{
RunSLSI(object, ...)
\method{RunSLSI}{default}(
object,
assay = NULL,
n = 50,
reduction.key = "SLSI_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
\method{RunSLSI}{Assay}(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.key = "SLSI_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
\method{RunSLSI}{Seurat}(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.name = "slsi",
reduction.key = "SLSI_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
}
\arguments{
\item{object}{An object}
\item{...}{Arguments passed to IRLBA irlba}
\item{assay}{Name of Assay SLSI is being run on}
\item{n}{Total Number of SLSI components to compute and store}
\item{reduction.key}{dimensional reduction key, specifies the string before
the number for the dimension names}
\item{graph}{Graph used supervised by SLSI}
\item{verbose}{Display messages}
\item{seed.use}{Set a random seed. Setting NULL will not set a seed.}
\item{features}{Features to compute SLSI on. If NULL, SLSI will be run
using the variable features for the Assay.}
\item{reduction.name}{dimensional reduction name}
}
\value{
Returns Seurat object with the SLSI calculation stored in the
reductions slot
}
\description{
Run a supervised LSI (SLSI) dimensionality reduction supervised by a
cell-cell kernel. SLSI is used to capture a linear transformation of peaks
that maximizes its dependency to the given cell-cell kernel.
}
\concept{dimensional_reduction}