Lightweight One-Line Resolving Microbial Ecology Program

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Documentation for package ‘LorMe’ version 2.0.2

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LorMe-package LorMe: Lightweight One-Line Resolving Microbial Ecology Program
$-method Access LorMe object elements via $
.DollarNames.LorMe Tab completion for LorMe $ access
.LorMe_opts Global options for LorMe pipeline analysis
.onLoad Accessed by 'getOption("LorMe")' or 'LorMe_options()'
add_tree Attach phylogenetic tree to the LorMe object
Alpha_diversity_calculator Calculate alpha diversity based on tax summary object
Alpha_diversity_calculator2 Calculate alpha diversity based on tax summary object or dataframe table
anova_report Print Analysis of Variance report
auto_signif_test Automatic significance test
circulation_lm Circulation of fitting Linear Models
color_scheme Get color scheme
combine_and_translate Combine data for visualization
community_plot Generate Community Composition Plot Based on Tax_summary Object
compare_plot Comparison plot generator This function help generate comparsion plot including bar plot, box plot, and violin plot
Deseq_analysis Deseq Analysis Function
Deseq_analysis2 Deseq analysis
differential_bar Generate Differential Bar Plot and Error bar Plot
Dimension_reduction Dimension_reduction: PCA, PCOA, and NMDS Analysis
Facet_group Tax summary object with Facet 2x2 Groups
Filter_function Filter OTU/ASV/metagenomic profile/gene profile by threshold
indicator_analysis Indicator Analysis
kruskal_report Print Kruskal-Wallis Rank Sum Test report
LorMe LorMe: Lightweight One-Line Resolving Microbial Ecology Program
LorMe-class LorMe S4 class
LorMe_defaults Restore LorMe global options to factory defaults
LorMe_options Change LorMe options
LorMe_pipeline One-stop microbial analysis pipeline for LorMe objects
manhattan Manhattan Plot Generator
Module_abundance Calculate network module abundance for each sample
Module_composition Pie chart for network module composition
nc Calculate Network Natural Connectivity
NC_remove Natural connectivity analysis
network_analysis Conduct Network analysis based on tax summary object
network_analysis2 Conduct Network analysis
network_stat Igraph network statistics
network_visual Network Visualization
network_visual_re Re-visualize network plot from 'network_visual' or 'network_withdiff'
network_withdiff Network Analysis with Differential Species
object_config Set taxonomy summary configuration
safe_run Running function with safe mode
show-method Show method for LorMe objects
structure_plot Visualize microbial community composition structure based on tax summary object
sub_tax_summary Subsetting tax summary objects
tax_summary Encapsulate meta file, feature tables and taxonomy annotation into tax summary object
tbRDA_analysis tbRDA analysis
testotu test otudata
theme_zg A classic theme for ggplot
Three_group Tax summary object with three groups
Top_taxa Calculate top taxa and others
Trans_from_microeco Convert a microeco object to a LorMe object
Trans_from_phylo Convert phyloseq object to LorMe object
Trans_to_microeco Convert a LorMe object to a microeco object
Trans_to_phylo Convert a LorMe object to a phyloseq object
Two_group Tax summary object with two groups
t_test_report Print Student's t-Test report
volcano_plot Generate Volcano plot base on Deseq_analysis or indicator_analysis results
wilcox_test_report Print Wilcoxon Rank Sum and Signed Rank Tests reprot