MRfulltable: Table of top microbial marker gene from linear model fit...

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

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	Output of fitFeatureModel or 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))

HCBravoLab/metagenomeSeq documentation built on Dec. 20, 2024, 4:06 p.m.