build_sra_submission: Create BioSamples Attributes and SRA Metadata Tables
In ressy/srahelper: SRA Helper

Description Usage Arguments Details Value

Create all required SRA metadata in one go from the given data frames and returns list of resulting data frames. This encapsulates both build_biosamples_from_template and build_metadata.

build_sra_submission(package_name, biosample_attrs,
  biosample_col_pairs = NULL, biosample_constants = NULL,
  metadata_attrs = NULL, metadata_col_pairs = NULL,
  metadata_constants = NULL, submission_accession = NULL)

`package_name`	name of BioSample Package for the template to use, as either the display name (e.g., "MIGS: cultured bacteria/archaea, human-associated; version 4.0") or the short name (e.g., "MIGS.ba.human-associated.4.0")
`biosample_attrs`	data frame of existing sample metadata to draw from for biological samples. Any names given in the `biosample_col_pairs` argument will be used to explicitly map column names from the existing data frame to the new data frame. Remaining columns with matching names will also be used. Other columns not in `biosample_col_pairs` or the template's fields are ignored.
`biosample_col_pairs`	named vector of column names in the existing data frame with names set to column names in the new data frame. Vector names that don't match known column names signify custom columns to add.
`biosample_constants`	vector of field names to match to constant values for all samples.
`metadata_attrs`	data frame of existing library metadata to draw from, analagous to `biosample_attrs`. If not specified, `biosample_attrs` wil be used.
`metadata_col_pairs`	named vector for metadata, as for `biosample_col_pairs`.
`metadata_constants`	named vector for metadata, as for `biosample_constants`.
`submission_accession`	the accession assigned by the submission portal for the submission, like "SUB####". Will be attached to the output data frames as an attribute if given.

If there is a one-to-one match between biological samples and sequencer samples, metadata_attrs can be left out and biosamples_attrs will be used for both spreadsheets.

list of data frames for BioSample Attributes and SRA Metadata.

ressy/srahelper documentation built on May 29, 2019, 11:03 p.m.