DESeq2_l2fc: Calculating log2 fold change for HTS-SIP data.

In SIPmg: Statistical Analysis to Identify Isotope Incorporating MAGs

Calculating log2 fold change for HTS-SIP data.

Description

The 'use_geo_mean' parameter uses geometric means on all non-zero abundances for estimateSizeFactors instead of using the default log-tranformed geometric means.

Usage

DESeq2_l2fc(
  physeq,
  density_min,
  density_max,
  design,
  l2fc_threshold = 0.25,
  sparsity_threshold = 0.25,
  sparsity_apply = "all",
  size_factors = "geoMean"
)

Arguments

physeq	Phyloseq object
density_min	Minimum buoyant density of the 'heavy' gradient fractions
density_max	Maximum buoyant density of the 'heavy' gradient fractions
design	design parameter used for DESeq2 analysis. See DESeq2::DESeq for more details.
l2fc_threshold	log2 fold change (l2fc) values must be significantly above this threshold in order to reject the hypothesis of equal counts.
sparsity_threshold	All OTUs observed in less than this portion (fraction: 0-1) of gradient fraction samples are pruned. A a form of indepedent filtering, The sparsity cutoff with the most rejected hypotheses is used.
sparsity_apply	Apply sparsity threshold to all gradient fraction samples ('all') or just heavy fraction samples ('heavy')
size_factors	Method of estimating size factors. 'geoMean' is from (Pepe-Ranney et. al., 2016) and removes all zero-abundances from the calculation. 'default' is the default for estimateSizeFactors. 'iterate' is an alternative when every OTU has a zero in >=1 sample.

Value

dataframe of HRSIP results

Examples

data(phylo.qSIP)


df_l2fc = DESeq2_l2fc(phylo.qSIP, density_min=1.71, density_max=1.75, design=~Isotope)

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