Microbial community dIversity and Network Analysis

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Documentation for package ‘mina’ version 1.2.0

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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.