无法打开用于绘制物理树的.biom文件

Question

尝试读取biom文件后：

rich_dense_biom  <-
  system.file("extdata", "D:\sample_otutable.biom", package = "phyloseq")

myData  <-
  import_biom(rich_dense_biom, treefilename, refseqfilename, parseFunction =
                parse_taxonomy_greengenes)

显示以下错误

Error in read_biom(biom_file = BIOMfilename) : 
  Both attempts to read input file:

either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.

Answer 1

你确定D:\sample_otutable.biom真的存在吗？是系统文件吗？

在R for Windows中，它至少更安全(如果不是必需的？)使用\\分隔文件路径

这对我很管用

library("devtools")
install_github("biom", "joey711")
library(biom)

biom.file <-
  "C:\\Users\\Mark Miller\\Documents\\R\\win-library\\3.3\\biom\\extdata\\min_dense_otu_table.biom"

my.data <- import_biom(BIOMfilename = biom.file)