R: Microbial community dIversity and Network Analysis

# Microbial community dIversity and Network Analysis

## Documentation for package ‘mina’ version 1.20.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

adj | Calculate the correlation adjacacency matrix.
adj-method | Calculate the adjacency matrix of 'norm' by correlation with matrix as input.
adj-method | Calculate the adjacency matrix of 'norm' by correlation with 'mina' class object as input.
adj_method_list | List of adjacency matix calculation methods/ orrelations supported in 'adj'
bs_pm | Inferring the network of different group of samples and test significance by permutation.
bs_pm-method | Inferring the network of different group of samples and test significance by permutation.
check_mina | Check the tab and des file. Return TRUE if they are NULL or both quantitative and descriptive files of same samples are included (i.e. the object is valid).
check_mina_de | Check the object and return TRUE if the object includes descriptive table contains the same samples as quantitative table.
check_mina_qu | Check the object and return TRUE if the object includes quantitative table.
cls_tab | Get the slot 'cls_tab'.
com_dis | Calculate the community dissimilarity / distance matrix.
com_dis-method | Calculate the community dissimilarity / distance matrix of the input matrix.
com_dis-method | Calculate the community dissimilarity / distance matrix of 'norm' with 'mina' class object as input.
com_dis_list | List of dissimilarity / distance supported in 'com_dis'. Dissimilarity / distance should be specified by exact string match.
com_plot | Visulization of components distance / dissimilarity in k dimension.
com_plot-method | Visulization of components distance / dissimilarity in k dimension.
com_r2 | Calculate the unexplained variance ratio using formula indicated in: Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26: 32-46.
com_r2-method | Function for unexplained variance ratio calculation indicated in Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26: 32-46.
cp_cor | Function for correlation coefficient calculation.
data-hmp | Internal testing data of HMP project, including quantitative table (hmp_otu) and descriptive table (hmp_des) for testing.
data-maize | Internal testing data of maize project, vegetative stage samples only, including quantitative table (maize_asv.rds) and descriptive table (maize_des.txt) for testing.
des | Setter and getter for the slot 'des', which is the description and meta data of rows in 'tab'.
des-method | Setter and getter for the slot 'des', which is the description and meta data of rows in 'tab'.
des<- | Setter and getter for the slot 'des', which is the description and meta data of rows in 'tab'.
des<--method | Setter and getter for the slot 'des', which is the description and meta data of rows in 'tab'.
dis | Setter and getter for the slot 'dis'.
dis-method | Setter and getter for the slot 'dis'.
dis<- | Setter and getter for the slot 'dis'.
dis<--method | Setter and getter for the slot 'dis'.
dis_bs | Getter for the slots 'dis_bs', 'dis_pm' and 'dis_stat'.
dis_pm | Getter for the slots 'dis_bs', 'dis_pm' and 'dis_stat'.
dis_stat | Getter for the slots 'dis_bs', 'dis_pm' and 'dis_stat'.
dmr | Dimensionality reduction of community dissimilarity / distance for visulization.
dmr-method | Dimensionality reduction of the distance matrix.
dmr-method | Dimensionality reduction of the 'dis' included in mina.
fit_tabs | Filter the quantitative and descriptive table to make them have the same samples, the intersect samples will be remained.
fit_tabs-method | Filter the quantitative and descriptive table to make them have the same samples, samples present in both tables are remained. If 'norm' table exist in the 'mina' object, descriptive table will be filtered again to only keep samples present in 'norm'.
get_net_cls_tab | Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.
get_net_cls_tab-method | Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.
get_r2 | Same function as 'com_r2' with matrix and corresponding descriptive table as input.
get_r2-method | Function for unexplained variance ratio calculation indicated in Anderson, M.J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecology, 26: 32-46.
get_rep | Get the representative community members by extracting the most abundant and prevalent compositions.
get_rep-method | Get the representative community members by extracting the most abundant and prevalent compositions.
get_rep-method | Get the representative community members.
hmp | Internal testing data of HMP project, including quantitative table (hmp_otu) and descriptive table (hmp_des) for testing.
hmp_des | Design file for HMP project, including 2711 samples in total.
hmp_otu | OTU table of HMP project, data downloaded from https://www.hmpdacc.org/hmp/HMQCP/
maize | Internal testing data of maize project, vegetative stage samples only, including quantitative table (maize_asv.rds) and descriptive table (maize_des.txt) for testing.
maize_asv | ASV table of maize project, vegetative stage samples only.
maize_asv2 | Subset of ASV table of maize project, ASVs appear in less than 100 samples were filtered for later analysis.
maize_des | Design file of maize project, vegetative stage samples only, including 528 samples in total.
maize_des2 | Subset of design file of maize project, 313 samples are included.
mina-class | Class "mina" includes the quantitative table and descriptive table.
net_cls | Network clustering of sparsed adjacacency matrix.
net_cls-method | Network clustering based on the sparsed adjacacency matrix.
net_cls-method | Network clustering based on the sparsed adjacacency matrix.
net_cls_tab | Get the cluster table 'cls_tab' from 'norm' and 'cls'.
net_cls_tab-method | Get the cluster table 'cls_tab' from quantitative table 'norm' and network clustering results 'cls'.
net_dis | Calculate the network distance of 'multi' and test the significance when 'perm' is defined.
net_dis-method | Calculate the network distance of 'multi' and test the significance when 'perm' is defined.
net_dis_indi | Calculate the network distance of bootstrap and permutation when appliable.
net_dis_indi-method | Calculate the network distance of bootstrap and permutation when appliable.
net_dis_pcoa | Visulization of spectra network distance as PCoA.
net_dis_pcoa-method | Visulization of spectra network distance as PCoA.
net_dis_plot | Visulization of network distance, average distances are used for tile plot.
net_dis_plot-method | Visulization of network distance, average distances are used for tile plot.
net_grp_cmp | Compare the group features between networks.
net_grp_cmp-method | Compare the group features between networks.
net_node_cmp | Compare the node features between networks.
net_node_cmp-method | Compare the node features between networks.
norm | Setter and getters for the slot 'norm', normalized 'tab' matrix.
norm-method | Setter and getters for the slot 'norm', normalized 'tab' matrix.
norm<- | Setter and getters for the slot 'norm', normalized 'tab' matrix.
norm<--method | Setter and getters for the slot 'norm', normalized 'tab' matrix.
norm_tab | Normalize the slot 'tab' for later analysis.
norm_tab-method | Normalize the quantitative matrix.
norm_tab-method | Normalize the quantitative table with mina input.
norm_tab_method_list | List of normalization methods supported in 'norm_tab'
pcoa_plot | Visulization of components distance / dissimilarity in k dimension.
pcoa_plot-method | Visulization of components distance / dissimilarity in k dimension.
tab | Setter and getter for the slot 'tab'.
tab-method | Setter and getter for the slot 'tab'.
tab<- | Setter and getter for the slot 'tab'.
tab<--method | Setter and getter for the slot 'tab'.
tina | TINA community dissimilarity used in 'com_dis'. Function for 'tina' dissimilarity/distance calculation. Modified from Schmidt et al., 2016.
tina-method | Function for 'tina' dissimilarity calculation. Modified from Schmidt et al., 2016. Person and Spearman could be used for correlation and weighted and unweighted Jaccard could be used for similarity calculation.