metagenomeSeq (version 1.14.0)

MRfulltable: Table of top microbial marker gene from linear model fit including sequence information

Description

Extract a table of the top-ranked features from a linear model fit. This function will be updated soon to provide better flexibility similar to limma's topTable. This function differs from link{MRcoefs} in that it provides other information about the presence or absence of features to help ensure significant features called are moderately present.

Usage

MRfulltable(obj, by = 2, coef = NULL, number = 10, taxa = obj$taxa, uniqueNames = FALSE, adjustMethod = "fdr", group = 0, eff = 0, numberEff = FALSE, ncounts = 0, file = NULL)

Arguments

obj

A list containing the linear model fit produced by lmFit through fitZig.

by

Column number or column name specifying which coefficient or contrast of the linear model is of interest.

coef

Column number(s) or column name(s) specifying which coefficient or contrast of the linear model to display.

number

The number of bacterial features to pick out.

taxa

Taxa list.

uniqueNames

Number the various taxa.

adjustMethod

Method to adjust p-values by. Default is "FDR". Options include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". See p.adjust for more details.

group

One of five choices: 0,1,2,3,4. 0: the sort is ordered by a decreasing absolute value coefficient fit. 1: the sort is ordered by the raw coefficient fit in decreasing order. 2: the sort is ordered by the raw coefficient fit in increasing order. 3: the sort is ordered by the p-value of the coefficient fit in increasing order. 4: no sorting.

eff

Filter features to have at least a "eff" quantile or number of effective samples.

numberEff

Boolean, whether eff should represent quantile (default/FALSE) or number.

ncounts

Filter features to those with at least 'counts' counts.

file

Name of output file, including location, to save the table.

Value

Table of the top-ranked features determined by the linear fit's coefficient.

See Also

fitZig fitFeatureModel MRcoefs MRtable fitPA

Examples

data(lungData)
k = grep("Extraction.Control",pData(lungData)$SampleType)
lungTrim = lungData[,-k]
lungTrim=filterData(lungTrim,present=30)
lungTrim=cumNorm(lungTrim,p=0.5)
smokingStatus = pData(lungTrim)$SmokingStatus
mod = model.matrix(~smokingStatus)
fit = fitZig(obj = lungTrim,mod=mod)
# head(MRfulltable(fit))
####
fit = fitFeatureModel(obj = lungTrim,mod=mod)
# head(MRfulltable(fit))