qSIP_atom_excess: Calculate atom fraction excess using q-SIP method

Description Usage Arguments Value Examples

View source: R/qSIP_atom_excess.R

Description

Calculate atom fraction excess using q-SIP method

Usage

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qSIP_atom_excess(physeq, control_expr, treatment_rep = NULL,
  isotope = "13C", df_OTU_W = NULL)

Arguments

physeq

A phyloseq object

control_expr

Expression used to identify control samples based on sample_data.

treatment_rep

Which column in the phyloseq sample data designates replicate treatments

isotope

The isotope for which the DNA is labeled with ('13C' or '18O')

df_OTU_W

Keep NULL

Value

A list of 2 data.frame objects. 'W' contains the weighted mean buoyant density (W) values for each OTU in each treatment/control. 'A' contains the atom fraction excess values for each OTU. For the 'A' table, the 'Z' column is buoyant density shift, and the 'A' column is atom fraction excess.

Examples

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# tranforming values
physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)

## Not run: 
# BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess(physeq_rep3_t,
                         control_expr='Treatment=="12C-Control"',
                         treatment_rep='Replicate')

## End(Not run)

nyoungb2/HTSSIP documentation built on April 10, 2018, 9:10 a.m.