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read_qiime2_feature_table

Source: R/read_qiime2_feature_table.R
read_qiime2_feature_table.Rd

Read a qiime2 qza containing bin data

Usage

read_qiime2_feature_table(
  qza,
  dir_path = NULL,
  remove_unpacked_artifacts = TRUE
)

Arguments

qza

file name, a qiime2 .qza file containing bin data.

dir_path

a string containing the name of directory where the artifacts files should be unpacked. Default = current working directory.

remove_unpacked_artifacts

boolean, When TRUE, the artifact's temporary directories will be removed after processing. Default = TRUE.

Value

A list containing artifact

Examples


if (requireNamespace("h5lite", quietly = TRUE)) {
  artifact <- read_qiime2_feature_table(strollur_example("table.qza"))

  # access the bin assignment table

  artifact$data

  # to create a `strollur` object with your data

  data <- new_dataset("my_data")

  assign(data = data, table = artifact$data, type = "bin")
  data
} else {
  message(paste(
    "To use this functionality you have to install the",
    "h5lite package."
  ))
}
#> Assigned 759 otu bins.
#> my_data:
#> 
#> 
#> Number of unique seqs: 759 
#> Total number of seqs: 157298 
#> 
#> Total number of samples: 34 
#> Total number of otus: 759 
#>