calc_wad: Calculation of weighted average densities

In bramstone/qSIP: Quantitative stable isotope probing for microbial ecology

Calculation of weighted average densities

Description

Calculates weighted average densities for each microbial taxa in each sample replicate

Usage

calc_wad(
  data,
  tax_id = c(),
  sample_id = c(),
  frac_id = c(),
  frac_dens = c(),
  frac_abund = c(),
  rel_abund = c(),
  grouping_cols = c()
)

Arguments

data	Data as a long-format data.table where each row represents a taxonomic feature within a single fraction.
tax_id	Column name specifying unique identifier for each taxonomic feature. Required.
sample_id	Column name specifying unique identifier for each replicate. Required
frac_id	Column name specifying fraction identifier. Does not have to be unique to each replciate because calc_wad will combine the unique sample ID with the fraction ID to generate a unique sample-fraction code. Required
frac_dens	Column name specifying buoyant density value for each fraction. Typically expressed as grams per milliliter from a cesium chloride density buffer. Required
frac_abund	Column name specifying abundance measurement for each fraction. Typically either the numbers of a target gene amplicon (e.g., 16S, ITS such as from qPCR) or DNA concentration (e.g., nanograms per microliter such as from a Qubit). Required
rel_abund	Column name specifying relativized abundance of each taxonomic feature, typically calculated after the removal of non-target lineages but before frequency filtering has been applied. Required
grouping_cols	Additional columns that should be included as important treatment groups in the output. Not strictly necessary for the calculation, but these will be utilized next to calculate fractional isotopic enrichment. Taxonomic information may be included here as well.

Details

The weighted average buoyant density (WAD) for taxon's DNA i in replicate j, designated as W_{ij}, is:

W_{ij} = \sum_{k=1}^{K} x_{jk} \cdot \left( \frac{y_{ijk}}{y_{ij}} \right)

Where y_{ij} = \sum_{k=1}^{K} y_{ijk}: Total abundance of taxon i in replicate j, by summing across all fractions (K)

y_{ijk} = P_{ijk} \cdot f_{jk}: The total abundance per \muL for taxon i in density fraction k of replicate i as calculated by it's relative abundance, P_{ijk} in that fraction multiplied by the total abundance of DNA or specific amplicons in that fraction, f_{jk}

x_{jk}: Density of fraction k of replicate j in (g cm^-3)

Value

calc_wad returns a reduced data.table where each row represents a taxonomic feature within a single replicate. The following columns are produced: weighted average densities (wad), weighted variance of densities (wvd), and replicate-level abundances (abund). wad values < 0 are removed.

The wvd term produced is the weighted variance in density, essentially a measure of how spread-out a feature's WAD value is. It is not strictly necessary to calculate fractional enrichment. It can sometimes be useful as a diagnostic of the quality of a feature’s density estimate.

Abundances are expressed in the same unit as fraction-level abundance measures of the community. For example, if fraction-level abundances were made using qPCR of a target gene (e.g., 16S or ITS), abundances represent the proportion of that gene attributed to a given taxon. If fraction-level abundances were made using DNA concentrations (e.g., such as from a Qubit measure), then the abund column is an expression of a taxon's proportional contribution to DNA concentration.

References

Hungate, Bruce, et al. 2015. Quantitative microbial ecology through stable isotope probing. Applied and Environmental Microbiology 81: 7570 - 7581.

Examples

 # Load in example data
 data(example_qsip)

 # relativize sequence abundances (should be done after taxonomic filtering)
 example_qsip[, rel_abund := seq_abund / sum(seq_abund), by = sampleID]

 # calculate weighted average densities
 wads <- calc_wad(example_qsip,
                  tax_id = 'asv_id', sample_id = 'sampleID', frac_id = 'fraction',
                  frac_dens = 'Density.g.ml', frac_abund = 'avg_16S_g_soil',
                  rel_abund = 'rel_abund',
                  grouping_cols = c('treatment', 'isotope', 'iso_trt', 'Phylum'))

bramstone/qSIP documentation built on Nov. 22, 2023, 9:11 p.m.