Man pages for blue-moon22/resistomeAnalysis
Resistome Analysis
| bootstrap_CI | Calculates the 95% confidence intervals for each bootstrap... |
| bootstrap_percentage | Bootstraps the samples and recalculates proportion of samples... |
| combineBedtools | Combines mapping data with metadata and CARD data |
| combineCARDBlast | Combines CARD blast output files with metadata and CARD data |
| combineMetaphlanandARG | Combine a dataframe containing mapping data and metadata data... |
| combineMetaphlanSamples | Combines metaphlan2 output data |
| combinePATRICBlast | Combines PATRIC blast output files with metadata and PATRIC... |
| combineSubsampled | Combines proportions and confidence intervals from... |
| createCircularGraph | Create a circular graph showing the core ARGs for each ARG... |
| createPairedData | Creates a dataframe of paired sample types with a column... |
| createRPKMHeatmap | Draws a heatmap from a dataframe of ARG abundance for every... |
| createUSDendrogram | Draws a dendrogram of hierachical clustering of ARG rpkm for... |
| drawCoreARGs | Draw a circular graph showing the core ARGs for each ARG... |
| drawCorrelationHeatmap | Draws a heatmap from a dataframe of correlated ARGs and taxa |
| filterBlastOutput | Filters blast output file |
| getBestBlastHit | Gets the best BLAST hit from overlapping ORFs |
| getProportion | Creates a dataframe that shows the proportion of samples that... |
| getRelativeAbundance | Get relative abundance of total rpkm per Location, sample... |
| getRelativeAbundanceIndividuals | Get relative abundance of total rpkm per individual, sample... |
| getSpearmanCorrelation | Get a dataframe of correlated ARGs and taxa using Spearman's... |
| g_legend | Extract legend from ggplot object |
| joinProportionAndBootstrap | Merges dataframes of proportion of samples containing a... |
| mergeData | Merge dataframes proportion and confidence intervals of... |
| plotARGClassAbundance | Plot stacked bar charts of the relative abundance of total... |
| plotGraph | Plot scatter graph of proportion against DDD per 1000 |
| plotIndividualAbundance | Plot stacked bar charts of the relative abundance of total... |
| plotMultipleARGRichnessGraphs | Plots multiple box and whisker diagrams of the ARG richness... |
| plotMultipleRPKM | Plots multiple box and whisker diagrams of total RPKM between... |
| plotPercentages | Plots a bar chart of the porportions of samples that contain... |
| plotResistotypes | Plot principal coordinates with resistotype labels |
| plotRPKM | Plots a box and whisker diagram between paired samples types |
| plotScatter | Plots a scatter plots of the porportions of samples that... |
| plotVolcano | Plot Volcano plots of differential analysis |
| readMappingData | Read a csv file of combined mapping data and metadata |
| readResistanceMapUseData | Read resistanceMap use data |
| runDESeq2 | Runs differential analysis using DESeq2 for a Location... |
| runPrincipleCoordinateAnalysis | Run principal coordinate analysis on mapping data and... |
| runTtest | Runs a t-test between groups from a dataframe of paired... |
