Man pages for pmartR/pmartRseq
Analysis and Visualization of 16S Data

abundance_calcCalculates Abundance
alphaDiv_calcCalculates Alpha Diversity Indices
applyFiltApply a filter to an omicsData object
applyFilt_workerRemove items that need to be filtered out
as.seqDataConvert Data to Appropriate pmartRseq Class
CLR_NormCentered-log Ratio Normalization of count data
count_based_filterCount filter object
countSTATStatistical tests for count data
CSS_NormCumulative sum scaling normalization of count data
detect_modulesDetect modules for Network
effsp_calcCalculates Effective Species
evenness_calcCalculates Evenness Indices
group_designationCreates Data Frame for Group Membership Based on Specified...
import_seqDataImport rRNA (16S/ITS/18S), metatranscript, or metagenomic...
indsp_calcComputes Indicator Species Analysis for Count Data
jaccard_calcCalculates Jaccard Index
Log_NormLog transformation of count data
med_scounts_normNormalization of count data via DESeq scale factors
metadata_based_filterMetadata filter object
mod_envFunction to calculate module eigen vectors and correlate...
network_calcCalculates Correlations
network_indicesCalculate Indices (metrics) for Network
network_plotGenerate Network Plot
normalize_dataNormalize data
plot_all_diffabunPlot all differential abundance results
plot_indspPlot Indicator species Analysis Results
plot_pmartRseqProduce a plot of an omicsData Object
pmartRseqpmartRseq: A pipeline package that enables a reproducible...
pmartRseq_aldex2Modified version of ALDEx2 for pmartRseq
pmartRseq_DESeq2DESeq2 analysis of omicsData objects
pmartRseq_edgeRedgeR analysis of omicsData objects
pmartRseq_igraphCalculates a network graph
pmartRseq_NMDSNMDS plot for beta diversity
pmartRseq_to_veganTransforms an omicsData object into a vegan data object
poisson_normNormalization of count data via Poisson Sampling
Quant_NormQuantile normalization of count data
RarefyRarefying of count data
reportCreates a report for pmartRseq objects
richness_calcCalculates Richness
sample_based_filterSample filter object
split_emetaSplits an e_meta column into separate columns
summary-pmartRseqProduce a basic summary of an pmartRseq S3 Object
taxa_rollupRoll up data to a specified taxonomic level
TMM_NormTrimmed Mean of M Values normalization of count data
TSS_NormTotal sum scaling normalization of count data
pmartR/pmartRseq documentation built on Feb. 15, 2018, 11:03 a.m.