Statistical Analysis to Identify Isotope Incorporating Metagenomic Features

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Documentation for package ‘SIPmg’ version 3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

as.Num	The following function is adapted from HTSSIP R package conversion to numeric
atomX	Atom fraction excess table
calc_atom_excess_MAGs	Calculate atom fraction excess
calc_Mheavymax_MAGs	Calculate Mheavymax
coverage_normalization	Normalize feature coverages to estimate absolute abundance or relative coverage using MAG/contig coverage values with or without multiplying total DNA concentration of the fraction
DESeq2_l2fc	Calculating log2 fold change for HTS-SIP data.
df_atomX_boot	Bootstrapped atom fraction excess table
filter_l2fc	Filter l2fc table
filter_na	Remove MAGs with NAs from atomX table
fractions	Fractions table
f_tibble	Coverage table
GC_content	GC_content table
HRSIP	(MW-)HR-SIP analysis
incorporators_taxonomy	Isotope incorporator list with GTDB taxonomy
mag.table	MAG abundance table in phyloseq format
phylo.qSIP	Master phyloseq object
phylo.table	Master phyloseq object using the MAG phyloseq objects
phyloseq2df	The following function is adapted from HTSSIP R package phyloseq data object conversion to data.frame
phyloseq2table	The following function is adapted from HTSSIP R package Phyloseq conversion to a ggplot-formatted table
qSIP_atom_excess_format_MAGs	Reformat a phyloseq object of qSIP_atom_excess_MAGs analysis
qSIP_atom_excess_MAGs	Calculate atom fraction excess using q-SIP method
qSIP_bootstrap_fcr	Calculate adjusted bootstrap CI after for multiple testing for atom fraction excess using q-SIP method. Multiple hypothesis tests are corrected by
sample.table	phyloseq-styled sample table
samples.object	Fractions table in phyloseq format
scale_features_lm	Scale feature coverage values to estimate their absolute abundance
scale_features_rlm	Scale feature coverage values to estimate their absolute abundance
sequins	Sequins table
seq_dil	Sequins dilution table
tax.table	phyloseq taxa table from GTDB taxonomy input
taxonomy.object	Taxonomy table in phyloseq format
taxonomy_tibble	Taxonomy table