bidsr (version 0.1.1)

get_bids_samples: 'BIDS' samples table class

Description

A tabular containing a list of samples and their metadata. The class is a child class of BIDSTabular, hence see the methods there. The original specification is at https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#samples-file.

Usage

get_bids_samples(x, ...)
BIDSTabularSamples(content, meta = NULL)

Value

A BIDSTabularSamples instance inheriting BIDSTabular.

Arguments

x

R object such as file path, project instances, etc.

...

passed to other methods or ignored

content, meta

see BIDSTabular

Author

Zhengjia Wang

Examples

# basic
tabular <- BIDSTabularSamples(
  data.frame(
    sample_id = "sample-001",
    participant_id = "sub-001",
    sample_type = "cell line"
  )
)
tabular


# convert existing tabular
tabular <- BIDSTabular(
  data.frame(
    sample_id = "sample-001",
    participant_id = "sub-001",
    sample_type = "cell line"
  )
)
tabular <- as_bids_tabular(tabular, cls = BIDSTabularSamples)


# save to tsv
tsv <- file.path(tempdir(), "samples.tsv")
paths <- save_bids_tabular(tabular, tsv)
print(paths)

# use base R to read
read.table(tsv, header = TRUE, na.strings = "n/a")

# get sidecar
cat(readLines(paths$sidecar_path), sep = "\n")

# clean up
unlink(tsv)
unlink(paths$sidecar_path)