Package: mina 1.13.0

Rui Guan

mina: Microbial community dIversity and Network Analysis

An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.

Authors:Rui Guan [aut, cre], Ruben Garrido-Oter [ctb]

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# Install 'mina' in R:
install.packages('mina', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/guan06/mina/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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.

On BioConductor:mina-1.13.0(bioc 3.20)mina-1.12.0(bioc 3.19)

bioconductor-package

41 exports 0.49 score 86 dependencies

Last updated 2 months agofrom:07cc1c7c7f

Exports:.dmradjadj_method_listbs_pmcheck_minacheck_mina_decheck_mina_qucls_tabcom_discom_dis_listcom_plotcom_r2cp_cordesdes<-disdis_bsdis_pmdis_statdis<-dmrfit_tabsget_net_cls_tabget_r2get_repnet_clsnet_cls_tabnet_disnet_dis_indinet_dis_pcoanet_dis_plotnet_grp_cmpnet_node_cmpnormnorm_tabnorm_tab_method_listnorm<-pcoa_plottabtab<-tina

Dependencies:apclusterbackportsbase64encBHbiganalyticsbiglmbigmemorybigmemory.sribslibcachemcheckmatecliclustercodetoolscolorspacedata.tableDBIdigestevaluateexpmfansifarverfastmapfontawesomeforeachforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMCLmemoisemgcvmimemunsellnlmennetparallelDistpillarpkgconfigplyrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rlangrmarkdownrpartRSpectrarstudioapisassscalesstringistringrtibbletinytexutf8uuidvctrsviridisviridisLitewithrxfunyaml

Microbial dIversity and Network Analysis with mina

Rui Guan

Rendered frommina.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-10-18
Started: 2020-03-06

Readme and manuals

Help Manual

Help pageTopics
Calculate the correlation adjacacency matrix.adj
List of adjacency matix calculation methods/ orrelations supported in 'adj'adj_method_list
Calculate the adjacency matrix of `norm` by correlation with matrix as input.adj,matrix,ANY-method adj,matrix,character-method
Calculate the adjacency matrix of `norm` by correlation with `mina` class object as input.adj,mina,ANY-method adj,mina,character-method
Inferring the network of different group of samples and test significance by permutation.bs_pm
Inferring the network of different group of samples and test significance by permutation.bs_pm,mina,ANY-method bs_pm,mina,character-method
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
Check the object and return TRUE if the object includes descriptive table contains the same samples as quantitative table.check_mina_de
Check the object and return TRUE if the object includes quantitative table.check_mina_qu
Get the slot `cls_tab`.cls_tab
Calculate the community dissimilarity / distance matrix.com_dis
List of dissimilarity / distance supported in 'com_dis'. Dissimilarity / distance should be specified by exact string match.com_dis_list
Calculate the community dissimilarity / distance matrix of the input matrix.com_dis,matrix,ANY-method com_dis,matrix,character-method
Calculate the community dissimilarity / distance matrix of `norm` with `mina` class object as input.com_dis,mina,ANY-method com_dis,mina,character-method
Visulization of components distance / dissimilarity in k dimension.com_plot
Visulization of components distance / dissimilarity in k dimension.com_plot,mina,ANY-method com_plot,mina,character-method
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
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.com_r2,mina,ANY-method com_r2,mina,character-method
Function for correlation coefficient calculation.cp_cor
Internal testing data of HMP project, including quantitative table (hmp_otu) and descriptive table (hmp_des) for testing.data-hmp hmp
Internal testing data of maize project, vegetative stage samples only, including quantitative table (maize_asv.rds) and descriptive table (maize_des.txt) for testing.data-maize maize
Setter and getter for the slot `des`, which is the description and meta data of rows in `tab`.des des,mina-method des<- des<-,mina-method
Getter for the slots `dis_bs`, `dis_pm` and `dis_stat`.dis_bs dis_pm dis_stat
Setter and getter for the slot `dis`.dis dis,mina-method dis<- dis<-,mina-method
Dimensionality reduction of community dissimilarity / distance for visulization.dmr
Dimensionality reduction of the distance matrix.dmr,matrix-method
Dimensionality reduction of the `dis` included in mina.dmr,mina-method
Filter the quantitative and descriptive table to make them have the same samples, the intersect samples will be remained.fit_tabs
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`.fit_tabs,mina-method
Get the cluster table `cls_tab` from quantitative table `norm` and network clustering results `cls`.get_net_cls_tab
Get the cluster table `cls_tab` from quantitative table `norm` and network clustering results `cls`.get_net_cls_tab,matrix,data.frame-method
Same function as `com_r2` with matrix and corresponding descriptive table as input.get_r2
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_r2,matrix,ANY,ANY-method get_r2,matrix,data.frame,ANY-method get_r2,matrix,data.frame,character-method
Get the representative community members by extracting the most abundant and prevalent compositions.get_rep get_rep,matrix-method
Get the representative community members.get_rep,mina-method
Design file for HMP project, including 2711 samples in total.hmp_des
OTU table of HMP project, data downloaded from https://www.hmpdacc.org/hmp/HMQCP/hmp_otu
ASV table of maize project, vegetative stage samples only.maize_asv
Subset of ASV table of maize project, ASVs appear in less than 100 samples were filtered for later analysis.maize_asv2
Design file of maize project, vegetative stage samples only, including 528 samples in total.maize_des
Subset of design file of maize project, 313 samples are included.maize_des2
Class "mina" includes the quantitative table and descriptive table.mina-class
Network clustering of sparsed adjacacency matrix.net_cls
Get the cluster table 'cls_tab' from `norm` and `cls`.net_cls_tab
Get the cluster table `cls_tab` from quantitative table `norm` and network clustering results `cls`.net_cls_tab,mina-method
Network clustering based on the sparsed adjacacency matrix.net_cls,matrix,ANY-method net_cls,matrix,character-method
Network clustering based on the sparsed adjacacency matrix.net_cls,mina,ANY-method net_cls,mina,character-method
Calculate the network distance of `multi` and test the significance when `perm` is defined.net_dis
Calculate the network distance of bootstrap and permutation when appliable.net_dis_indi net_dis_indi,character,ANY-method net_dis_indi,character,character-method
Visulization of spectra network distance as PCoA.net_dis_pcoa net_dis_pcoa,character-method
Visulization of network distance, average distances are used for tile plot.net_dis_plot net_dis_plot,mina-method
Calculate the network distance of `multi` and test the significance when `perm` is defined.net_dis,mina,ANY-method net_dis,mina,character-method
Compare the group features between networks.net_grp_cmp net_grp_cmp,character-method
Compare the node features between networks.net_node_cmp net_node_cmp,character,character-method
Normalize the slot `tab` for later analysis.norm_tab
List of normalization methods supported in 'norm_tab'norm_tab_method_list
Normalize the quantitative matrix.norm_tab,matrix,character-method
Normalize the quantitative table with mina input.norm_tab,mina,ANY-method norm_tab,mina,character-method
Setter and getters for the slot `norm`, normalized `tab` matrix.norm norm,mina-method norm<- norm<-,mina-method
Visulization of components distance / dissimilarity in k dimension.pcoa_plot pcoa_plot,list,data.frame,character-method
Setter and getter for the slot `tab`.tab tab,mina-method tab<- tab<-,mina-method
TINA community dissimilarity used in 'com_dis'. Function for `tina` dissimilarity/distance calculation. Modified from Schmidt et al., 2016.tina
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.tina,matrix-method