获取RNA速率

> RunVelocity
function (object, spliced = "spliced", unspliced = "unspliced", 
    ambiguous = NULL, spliced.average = 0.2, unspliced.average = 0.05, 
    reduction = "pca", group.by = "ident", cells = NULL, graph = NULL, 
    ncores = 1, verbose = TRUE, ...) 
{
    CheckPackage(package = "velocyto-team/velocyto.R", repository = "github")
    clusters <- FetchData(object = object, vars = group.by)[, 
        , drop = TRUE]
    names(x = clusters) <- colnames(x = object)
    if (!is.factor(x = clusters)) {
        clusters <- as.factor(x = clusters)
    }
    if (verbose) {
        message("Filtering genes in the spliced matrix")
    }
    spliced.matrix <- velocyto.R::filter.genes.by.cluster.expression(emat = GetAssayData(object = object, 
        assay = spliced), clusters = clusters, min.max.cluster.average = spliced.average)
    if (verbose) {
        message("Filtering genes in the unspliced matrix")
    }
    unspliced.matrix <- velocyto.R::filter.genes.by.cluster.expression(emat = GetAssayData(object = object, 
        assay = unspliced), clusters = clusters, min.max.cluster.average = unspliced.average)
    if (verbose) {
        message("Calculating embedding distance matrix")
    }
    cell.dist <- as.dist(m = 1 - velocyto.R::armaCor(mat = t(x = Embeddings(object = object, 
        reduction = reduction))))
    args <- list(...)
    defaults <- as.list(x = formals(fun = velocyto.R::gene.relative.velocity.estimates))
    args <- args[intersect(x = names(x = args), y = names(x = defaults))]
    defaults.use <- setdiff(x = names(x = defaults), y = names(x = args))
    args[defaults.use] <- defaults[defaults.use]
    args$emat <- spliced.matrix
    args$nmat <- unspliced.matrix
    args$smat <- ambiguous %iff% GetAssayData(object = object, 
        assay = ambiguous)
    args$steady.state.cells <- cells %||% colnames(x = object)
    args$cell.dist <- cell.dist
    args$cellKNN <- graph %iff% object[[graph]]
    args$n.cores <- ncores
    args$verbose <- verbose
    sink(file = stderr(), type = "output")
    on.exit(expr = sink())
    cd <- do.call(what = velocyto.R::gene.relative.velocity.estimates, 
        args = args)
    Tool(object = object) <- cd
    return(object)
}
<bytecode: 0x000001ec81b7eb40>
<environment: namespace:SeuratWrappers>

里面有个gene.relative.velocity.estimates函数

所以，认为是deltaE

result <- as.data.frame(vel$deltaE)
result[1:5,1:5]

得到速率