OTU_qPCR_trans: Transform OTU counts based on qPCR data

Description Usage Arguments Details Value Examples

View source: R/qSIP_trans.R

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

1
2
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

1
2
3
4

HTSSIP documentation built on May 29, 2017, 5:34 p.m.

Search within the HTSSIP package
Search all R packages, documentation and source code