qSIP_atom_excess_MAGs {SIPmg} | R Documentation |
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)
[Package SIPmg version 1.4.1 Index]