FindSVGs.Rd
Identifies features that have spatially variation along spots using SPARK-X.
FindSVGs(seu, nfeatures=2000, covariates=NULL, num_core=1, verbose=TRUE)
an object of class "Seurat".
a positive integer, means how many spatially variable genes to be chosen. If there are less than 2000 features in seu, then all features are identified.
a covariate matrix named control variable matrix whose number of rows is equal to the number of columns of seu.
an optional positive integer, specify the cores used for identifying the SVGs in parallel.
an optional logical value, whether output the related information.
Nothing
return a revised Seurat object by adding three columns named "is.SVGs", "order.SVGs" and "adjusted.pval.SVGs" in the meta.features of default Assay.
Zhu, J., Sun, S., Zhou, X.: Spark-x: non-parametric modeling enables scalable and robust detection of spatialexpression patterns for large spatial transcriptomic studies. Genome Biology 22(1), 1-25 (2021)
nothing
seu<-gendata_RNAExp(height=20, width=20,p=200, K=4)
seu<-FindSVGs(seu, nfeatures=100)
#> Find the spatially variables genes by SPARK-X...
#> ## ===== SPARK-X INPUT INFORMATION ====
#> ## number of total samples: 400
#> ## number of total genes: 200
#> ## Running with single core, may take some time
#> ## Testing With Projection Kernel
#> ## Testing With Gaussian Kernel 1
#> ## Testing With Gaussian Kernel 2
#> ## Testing With Gaussian Kernel 3
#> ## Testing With Gaussian Kernel 4
#> ## Testing With Gaussian Kernel 5
#> ## Testing With Cosine Kernel 1
#> ## Testing With Cosine Kernel 2
#> ## Testing With Cosine Kernel 3
#> ## Testing With Cosine Kernel 4
#> ## Testing With Cosine Kernel 5
topSVGs(seu)
#> [1] "gene91" "gene99" "gene31" "gene61" "gene106"