最近在跑的方法需要.h5作为输入文件,就学习了一下怎么创建.h5文件,原有数据结构如下:
生成单组学.h5文件的代码如下:
library(rhdf5)
library(dplyr)
library(patchwork)
rna.data <- Read10X(data.dir='Processed_dataset/RNA',gene.column = 1)
atac.data <- Read10X(data.dir='Processed_dataset/ATAC',gene.column = 1)
dim(rna.data)
dim(atac.data)
###构建.h5文件
h5createFile("SNARE_cellline_atac.h5")
# Saving matrix information.
h5createGroup("SNARE_cellline_atac.h5","matrix")
h5write(atac.data@Dimnames[[2]] , "SNARE_cellline_atac.h5", "matrix/barcodes")
h5write(atac.data@x, "SNARE_cellline_atac.h5", "matrix/data")
dim(atac.data)
h5createGroup("SNARE_cellline_atac.h5","matrix/features")
h5write("genome", "SNARE_cellline_atac.h5", "matrix/features/_all_tag_keys")
Peaks <- rep("Peaks", length(atac.data@Dimnames[[1]]))
h5write(Peaks,"SNARE_cellline_atac.h5", "matrix/features/feature_type")
Genome <- rep("hg38", length(atac.data@Dimnames[[1]]))