In Goralsth/FloodLight:
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(FloodLight)
library(Seurat)
library(SeuratData)
SeuratData::InstallData("pbmc3k")
ref<-pbmc3k@assays$RNA@counts
cluster_ID<- pbmc3k@meta.data
as.data.frame(cluster_ID)
spots<-generate_spots(ref, cluster_ID)
Markers<-find_markers(ref)
Markers<-marker_column_names(cluster_ID,"seurat_annotations",ref)
Markers_Thresholded<-thresholding_markers(Markers, 0.6)
Subset_Counts<-Subset_Expression(Markers_Thresholded,ref, 1.5)
deconvolute_using_NNLS(Subset_Counts,spots)
Goralsth/FloodLight documentation built on April 20, 2022, 12:42 a.m.
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knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(FloodLight) library(Seurat) library(SeuratData) SeuratData::InstallData("pbmc3k") ref<-pbmc3k@assays$RNA@counts cluster_ID<- pbmc3k@meta.data as.data.frame(cluster_ID)
spots<-generate_spots(ref, cluster_ID) Markers<-find_markers(ref) Markers<-marker_column_names(cluster_ID,"seurat_annotations",ref) Markers_Thresholded<-thresholding_markers(Markers, 0.6) Subset_Counts<-Subset_Expression(Markers_Thresholded,ref, 1.5) deconvolute_using_NNLS(Subset_Counts,spots)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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