metagenomeSeq-package |
Statistical analysis for sparse high-throughput sequencing |
aggregateByTaxonomy |
Aggregates a MRexperiment object or counts matrix to a particular level. Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts to the desired level using the aggfun function (default colSums). Possible aggfun alternatives include colMeans and colMedians. |
aggTax |
Aggregates a MRexperiment object or counts matrix to a particular level. Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a MRexperiment and a particular featureData column (i.e. 'genus') will aggregate counts to the desired level using the aggfun function (default colSums). Possible aggfun alternatives include colMeans and colMedians. |
biom2MRexperiment |
Biome to MRexperiment objects |
calculateEffectiveSamples |
Estimated effective samples per feature |
colMeans-method |
Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
colSums-method |
Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
correctIndices |
Calculate the correct indices for the output of correlationTest |
correlationTest |
Pairwise correlation for each row of a matrix or MRexperiment object |
corTest |
Pairwise correlation for each row of a matrix or MRexperiment object |
cumNorm |
Cumulative sum scaling factors. |
cumNormMat |
Cumulative sum scaling factors. |
cumNormStat |
Cumulative sum scaling percentile selection |
cumNormStatFast |
Cumulative sum scaling percentile selection |
doCountMStep |
Compute the Maximization step calculation for features still active. |
doEStep |
Compute the Expectation step. |
doZeroMStep |
Compute the zero Maximization step. |
exportMat |
Export the normalized MRexperiment dataset as a matrix. |
exportMatrix |
Export the normalized MRexperiment dataset as a matrix. |
exportStats |
Various statistics of the count data. |
expSummary |
Access MRexperiment object experiment data |
expSummary-method |
Access MRexperiment object experiment data |
filterData |
Filter datasets according to no. features present in features with at least a certain depth. |
fitDO |
Wrapper to calculate Discovery Odds Ratios on feature values. |
fitMeta |
Computes a slightly modified form of Metastats. |
fitPA |
Wrapper to run fisher's test on presence/absence of a feature. |
fitZig |
Computes the weighted fold-change estimates and t-statistics. |
genusPlot |
Basic plot function of the raw or normalized data. |
getCountDensity |
Compute the value of the count density function from the count model residuals. |
getEpsilon |
Calculate the relative difference between iterations of the negative log-likelihoods. |
getNegativeLogLikelihoods |
Calculate the negative log-likelihoods for the various features given the residuals. |
getPi |
Calculate the mixture proportions from the zero model / spike mass model residuals. |
getZ |
Calculate the current Z estimate responsibilities (posterior probabilities) |
isItStillActive |
Function to determine if a feature is still active. |
libSize |
Access sample depth of coverage from MRexperiment object |
libSize-method |
Access sample depth of coverage from MRexperiment object |
load_biom |
Load objects organized in the Biome format. |
load_meta |
Load a count dataset associated with a study. |
load_metaQ |
Load a count dataset associated with a study set up in a Qiime format. |
load_phenoData |
Load a clinical/phenotypic dataset associated with a study. |
lungData |
OTU abundance matrix of samples from a smoker/non-smoker study |
makeLabels |
Function to make labels simpler |
metagenomeSeq |
Statistical analysis for sparse high-throughput sequencing |
metagenomicLoader |
Load a count dataset associated with a study. |
mouseData |
OTU abundance matrix of mice samples from a diet longitudinal study |
MRcoefs |
Table of top-ranked microbial marker gene from linear model fit |
MRcounts |
Accessor for the counts slot of a MRexperiment object |
MRcounts-method |
Accessor for the counts slot of a MRexperiment object |
MRexperiment-class |
Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
MRexperiment2biom |
MRexperiment to biom objects |
MRfulltable |
Table of top microbial marker gene from linear model fit including sequence information |
MRtable |
Table of top microbial marker gene from linear model fit including sequence information |
newMRexperiment |
Create a MRexperiment object |
normFactors |
Access the normalization factors in a MRexperiment object |
normFactors-method |
Access the normalization factors in a MRexperiment object |
phenoData |
Load a clinical/phenotypic dataset associated with a study. |
plotCorr |
Basic correlation plot function for normalized or unnormalized counts. |
plotFeature |
Basic plot function of the raw or normalized data. |
plotGenus |
Basic plot function of the raw or normalized data. |
plotMRheatmap |
Basic heatmap plot function for normalized counts. |
plotOrd |
Plot of either PCA or MDS coordinates for the distances of normalized or unnormalized counts. |
plotOTU |
Basic plot function of the raw or normalized data. |
plotRare |
Plot of rarefaction effect |
posterior.probs |
Access the posterior probabilities that results from analysis |
posterior.probs-method |
Access the posterior probabilities that results from analysis |
qiimeLoader |
Load a count dataset associated with a study set up in a Qiime format. |
rowMeans-method |
Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
rowSums-method |
Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
settings2 |
Settings for the fitZig function |
uniqueFeatures |
Table of features unique to a group |
zigControl |
Settings for the fitZig function |
[-method |
Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |