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qSIP sample data class

Source: R/qsip_objects.R
qsip_sample_data.Rd

The qsip_sample_data object holds validated sample metadata.

Usage

qsip_sample_data(
  data,
  sample_id = "sample_id",
  source_mat_id = "source_mat_id",
  gradient_position = "gradient_position",
  gradient_pos_density = "gradient_pos_density",
  gradient_pos_amt = "gradient_pos_amt",
  gradient_pos_rel_amt = ""
)

Arguments

data

(dataframe) Metadata for samples/fractions

sample_id

(string) The unique sample ID

source_mat_id

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

gradient_position

(string) Column name with the fraction position

gradient_pos_density

(string) Column name with the gradient density

gradient_pos_amt

(string) Column name with a total amount per fraction, either qPCR copies or DNA

gradient_pos_rel_amt

(string) Column name with the relative fraction abundance compared to the total

Value

A validated object of the qsip_sample_data type

Details

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

In qSIP and MISIP, a "sample" is the post-fractionated material with metadata pertaining to the fractionation process. Sample metadata contains information about the sample and fractionation, such as the sample ID, the source material ID, the gradient position, the density, the amount recovered (e.g. DNA concentration or 16S copies), and the relative abundance of the fraction compared to the total.

Ideally, gradient_pos_amt should be reported as a mass value of DNA rather than a concentration. However, if the concentration is reported, the fraction_volume argument can be used to convert the gradient_pos_amt concentration to a mass value. For example, if the gradient_pos_amt is reported as ng/ul, and the fraction_volume is reported as 100 ul, then the gradient_pos_amt will be converted to ng.

Internally, qsip_sample_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.

There are several validation checks done on the data.frame:

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

  • The sample_id column must contain unique values per row

  • The gradient_position must container positive integers, or -1 is allowed to designate the sample as "bulk" or unfractionated

See also

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