使用示例 # 3.使用library(Seurat)library(SeuratDisk)setwd('/home/name/path_to_your_files/')# 转换 .h5ad 文件为 .h5seurat 文件Convert("./data/Global_lognormalised.h5ad",assay="RNA",dest="h5seurat",overwrite=TRUE)# 读取 .h5seurat 文件为 Seurat 对象seurat_object<-LoadH5Seurat("./data/Gl...
Convert html Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b587c1cc15/SeuratDisk/man/Convert.Rd:48: file link 'H5File' in package 'hdf5r' does not exist and so has been treated as a topic Rd warning: C:/Users/Laura/AppData/Local/Temp/RtmpYfM7JQ/R.INSTALL5b...
Then you can use Seurat's function as.Seurat() to convert your object to Seurat. I also had to specify the default parameter counts and data to fit my data. E.g. i had to specify adata_Seurat <- as.Seurat(ad, counts = "X", data = NULL) You can find the name of your counts...
Yes, the answer was that the convert function was trying to pull the scaled data and there was no argument we could find in the convert function that would change where it was pulling from, so it was always pulling the scaled 2000 variable genes only: Adding scale.data from RNA as X Tr...
Hello, I'm currently trying to read in a h5ad-file into R. Since seurats ReadH5ad()-function didn't work out for me, I tried to do it with seurat-disk. First I converted my file into a h5seurat-file: Convert("test.h5ad", dest = "h5seurat", overwrite = TRUE, assay="RNA")...
I am able to trying to convert anndata object from scanpy (h5ad) to h5seurat to seurat object. I can convert data.h5ad to h5seurat format using Convert(). However, when I try to run seurat_object <- LoadH5Seurat("data.h5seurat") I get th...