build_biosamples_from_template: Create BioSamples Table

Description Usage Arguments Value

Description

Create a new BioSamples table using a named template and existing sample attributes.

Usage

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build_biosamples_from_template(package_name, sample_attrs,
  submission = NULL, col_pairs = NULL, constants = NULL)

Arguments

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"). Call list_templates to see all the pre-installed templates by their short name.

sample_attrs

data frame of existing sample metadata to draw from. Any names given in the 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 col_pairs or the template's fields are ignored.

submission

the accession assigned by the submission portal for the submission, like "SUB####". Will be attached to the output data frame as an attribute.

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.

constants

vector of field names to match to constant values for all samples.

Value

data frame with BioSample attributes defined.


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