OTU_qPCR_trans: Transform OTU counts based on qPCR data

In nyoungb2/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

OTU counts in the phyloseq otu_table object will be normalized to sample totals (total sum scaling), then multiplied by the qPCR value associated with each sample. Thus, the qPCR table should have ONE value matching the OTU count table. Value matching between the OTU table & qPCR value table to set by sample_idx().

Usage

OTU_qPCR_trans(physeq, qPCR, sample_idx = "Sample",
  value_idx = "qPCR_tech_rep_mean")

Arguments

physeq	A phyloseq object
qPCR	Either a list or a data.frame of qPCR data. If a list, the list should include a 'summary' tag as is produced from qPCR_sim(). If a data.frame, the table should be formatted as the 'summary' table produced from qPCR_sim().
sample_idx	The qPCR table column index for matching to otu table samples.
value_idx	The qPCR table column index for qPCR values.

Details

Note: only the 'summa

Value

A phyloseq object with transformed OTU counts

Examples

# qPCR data simulation
data(physeq_rep3)
data(physeq_rep3_qPCR)
physeq_rep3_t = OTU_qPCR_trans(physeq_rep3, physeq_rep3_qPCR)

nyoungb2/HTSSIP documentation built on May 24, 2019, 11:51 a.m.