Statistical Analysis to Identify Isotope Incorporating MAGs

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Documentation for package ‘SIPmg’ version 1.4.1

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

Help Pages

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
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