qSIP_atom_excess_MAGs: Calculate atom fraction excess using q-SIP method

In SIPmg: Statistical Analysis to Identify Isotope Incorporating MAGs

Calculate atom fraction excess using q-SIP method

Description

Calculate atom fraction excess using q-SIP method

Usage

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

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
Gi	GC content of the MAG

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

data(phylo.qSIP,GC_content)
### Making atomx table

## Not run::
### BD shift (Z) & atom excess (A)
atomX = qSIP_atom_excess_MAGs(phylo.qSIP,
                         control_expr='Isotope=="12C"',
                         treatment_rep='Replicate',
                         Gi = GC_content)

SIPmg documentation built on March 7, 2023, 6:47 p.m.