Man pages for rusher321/rmeta
the function for my daily work
| ANCOM | Analysis of Composition of Microbiomes |
| ancombc | Differential abundance (DA) analysis for microbial absolute... |
| centorComp | centroComp compare the center distance between groups |
| checkOutlier | checkOutlier output the outlier value on a vector by quantile |
| clusterTrajector | clusterTrajector |
| combindfile | Combine the file list |
| comparePair | comparePair wilcox pair test for multi time point |
| corPlot | corPlot pheatmap to figure the correlation |
| cssMeta | Cumulative sum scaling |
| cumNormStatFast2 | cum Norm stat method form ANCOM_BC |
| CvLassomulti | CvLasso selsect feature on diffrent group |
| CvLassoResponse | CvLassoResponse select feature using lasso method , to... |
| distJSD | JSD distance to compute the jsd distance |
| elibtmmMeta | Elib-Trimmed Mean of M values |
| elibuqMeta | the effective library size using UQ (upper quartile) |
| feature_table_pre_process | feature_table_pre_process |
| filterPer | filterPer |
| getMetahlan2rank | getMetaphlan2rank get the phylum-species rank |
| ggcorr | correlation between pairwise |
| kBest | kBest to get the best k in non-supervision method |
| kBest2 | kBest2 |
| kwmeta | kwmeta |
| matchpairID | matchpair ID to match the sample ID for pair wilcox test |
| medraioMeta | median ratio normalization |
| mergeP | mergeP merge two dataframe ,who have diffrent colname &... |
| multiAdonis | multiAdonis for pair compare for multigroup use the adonis |
| multiplot | Multiplot this function to plot volcano based ggplot2 |
| mutivarOutlier | mutivarOutlier on a dataframe to select the outlier |
| myGeeAnalysis | myGeeAnalysis |
| myPcor | myPcor |
| myvolcano | plot volcano this function to plot volcano based ggplot2 |
| mywilcox_2t | mywilcox_2t wilcox pair test for 2 time point |
| nmdsFig | nmdsFig |
| nmdsFigEx | nmdsFigEx plot the nmds figure |
| pairNet | pairNet |
| pasteP | transform a vector to string |
| pcoaFig | pcoaFig |
| r2Twopartmodel | r2Twopartmodel |
| r2Twopartmodelcv | r2Twopartmodelcv add the cross validation process From The... |
| RankINT | Based-rank Inverse Normal Transformation The detail inf is... |
| renorm | renorm normalization the compsition data |
| rmetaSMOTE | rmetaSMOTE |
| simplenet | simpleNet |
| smote.exs2 | smote.exs2 this function from package DMwR smote.exs |
| smoteMatch | smoteMatch |
| sparccNet | sparccNet |
| splitMetaphlan2 | split the metaphlan2 dataset |
| summaryCvlasso | summaryCvlasso summary n repeat cvresponse result |
| summarySE | summarySE |
| tmmMeta | Trimmed Mean of M values |
| topTax | topTax plot the high abundance tax |
| tssMeta | Total-Sum Scaling |
| twopartEta | twopartEta to compute the partial eta or relative risk |
| twopartModel | twopartModel From The Gut Microbiome Contributes to a... |
| uqMeta | upper quartile normalization |
