Error when running function ICASpatial #1
Description
Environment
R version 4.3.1 (2023-06-16)
CFS Version: 0.9.7.2
Code I am using to run CFS
library(future)
library(Seurat)
library(enrichR)
library(CFS)
library(moments)
library(dplyr)
library(purrr)
sample_path <- "path/to/sample"
data <- Load10X_Spatial(
sample_path,
filename = "filtered_feature_bc_matrix.h5",
assay = "Spatial",
slice = "slice1",
filter.matrix = TRUE,
to.upper = FALSE,
image = NULL,
)
data[["percent.mt"]] <- PercentageFeatureSet(data, pattern = "^MT-")
data <- subset(data, subset = nFeature_Spatial >= 5500 & percent.mt <= 15)
data <- PrepNormData(data=data,organism="Hs",variable_features=2000)
data <- ICASpatial(data=data,ncis=100,maxit=600,method="icafast",kurtosis = 3,sd=3)Error message
Error in validObject(.Object): invalid class “DimReduc” object: rownames must be present in 'cell.embeddings'
Traceback:
1. ICASpatial(data = data, ncis = 100, maxit = 600, method = "icafast",
. kurtosis = 3, sd = 3)
2. RunICA(data, verbose = TRUE, nics = ncis, maxit = maxit, ica.function = method)
3. RunICA.Seurat(data, verbose = TRUE, nics = ncis, maxit = maxit,
. ica.function = method)
4. RunICA(object = object[[assay]], assay = assay, features = features,
. nics = nics, rev.ica = rev.ica, ica.function = ica.function,
. verbose = verbose, ndims.print = ndims.print, nfeatures.print = nfeatures.print,
. reduction.key = reduction.key, seed.use = seed.use, ...)
5. RunICA.Assay(object = object[[assay]], assay = assay, features = features,
. nics = nics, rev.ica = rev.ica, ica.function = ica.function,
. verbose = verbose, ndims.print = ndims.print, nfeatures.print = nfeatures.print,
. reduction.key = reduction.key, seed.use = seed.use, ...)
6. RunICA(object = data.use, assay = assay, nics = nics, rev.ica = rev.ica,
. ica.function = ica.function, verbose = verbose, ndims.print = ndims.print,
. nfeatures.print = nfeatures.print, reduction.key = reduction.key,
. seed.use = seed.use, ...)
7. RunICA.default(object = data.use, assay = assay, nics = nics,
. rev.ica = rev.ica, ica.function = ica.function, verbose = verbose,
. ndims.print = ndims.print, nfeatures.print = nfeatures.print,
. reduction.key = reduction.key, seed.use = seed.use, ...)
8. CreateDimReducObject(embeddings = cell.embeddings, loadings = feature.loadings,
. assay = assay, key = reduction.key)
9. new(Class = "DimReduc", cell.embeddings = embeddings, feature.loadings = loadings,
. feature.loadings.projected = projected, assay.used = assay,
. global = global, stdev = stdev, key = key, jackstraw = jackstraw,
. misc = misc)
10. initialize(value, ...)
11. initialize(value, ...)
12. validObject(.Object)
13. stop(msg, ": ", errors, domain = NA)
What can I be doing wrong?