qSIP_atom_excess: Calculate atom fraction excess using q-SIP method

In nick-youngblut/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

Calculate atom fraction excess using q-SIP method

Usage

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

# 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)

nick-youngblut/HTSSIP documentation built on May 23, 2019, 4:46 p.m.