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qSIP source data class

Source: R/qsip_objects.R
qsip_source_data.Rd

The qsip_source_data object holds validated source material metadata.

Usage

qsip_source_data(
  data,
  isotope = "isotope",
  isotopolog = "isotopolog",
  source_mat_id = "source_mat_id",
  timepoint = "NULL",
  total_abundance = "NULL",
  volume = "NULL"
)

Arguments

data

(dataframe) Source metadata

isotope

(string) Isotope name

isotopolog

(string) Isotopolog data

source_mat_id

(string) The unique ID for the biological subject or source

timepoint

(string) Timepoint data

total_abundance

(string) Total abundance data

volume

(string) Volume of the abundance data. Defaults to 1, but can be a ul volume if abundance data is given as a concentration

Value

A validated qsip_source_data object

Details

qsip_source_data() is not a typical function, but rather a class constructor that instantiates a new qsip_source_data object. The constructor takes a data.frame as input and returns a validated qsip_source_data object.

In qSIP and MISIP, "source material" is your original biological specimen that DNA was extracted from. This could be a soil sample, a plant, a mouse, etc. This is the pre-fractionated metadata, and post-fractionation metadata goes in the qsip_sample_data object.

Several validation checks are run on the input data:

  • The data argument must be a data.frame, including a tibble

  • The isotope, isotopolog, and source_mat_id arguments must be column names in the data.frame

  • The source_mat_id column must be unique

  • The isotope column must contain valid isotope names. "Valid" means they must be one of the types that the qSIP2 package has equations for, namely 12C/13C, 14N/15N and 16O/18O. Some non-isotope names are also valid, including "bulk", "unfractionated" and "T0".

Internally, qsip_source_data renames the metadata columns to be standardized to MISIP terminology. A data.frame with the standardized names can be extracted back out of the object using the get_dataframe() method, and the optional original_headers argument can be set to TRUE to return the original column names.

One column of metadata that is required although not used by qSIP2 is the isotopolog column. This column is required to capture complete metadata that is compliant with the MISIP standards. However, when running experiments with multiple isotopologs this column can be used to generate correct comparison groups using the show_comparison_groups() function.

See also

Other "qSIP Objects": qsip_data(), qsip_feature_data(), qsip_sample_data()