topTable-methods: Methods for topTable

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Methods for topTable. topTable extracts the top n most important features for a given classification or regression procedure

Usage

## S4 method for signature 'limma'
topTable(
  fit,
  n = 10,
  coef = 2,
  genelist = fit$genes,
  eb = fit[c("t", "p.value", "lods")],
  adjust.method = "BH",
  sort.by = "B",
  resort.by = NULL,
  p.value = 1,
  lfc = 0
)

## S4 method for signature 'MArrayLM'
topTable(
  fit,
  n,
  coef = 2,
  genelist = fit$genes,
  eb = fit[c("t", "p.value", "lods")],
  adjust.method = "BH",
  sort.by = "B",
  resort.by = NULL,
  p.value = 1,
  lfc = 0
)

## S4 method for signature 'tTest'
topTable(fit, n)

## S4 method for signature 'fTest'
topTable(fit, n)

Arguments

fit	object resulting from a classification or regression procedure
n	number of features that one wants to extract from a table that ranks all features according to their importance in the classification or regression model; defaults to 10 for limma objects
coef	column number or column name specifying which coefficient or contrast of the linear model is of interest. For topTable, can also be a vector of column subscripts, in which case the gene ranking is by F-statistic for that set of contrasts.
genelist	data frame or character vector containing gene information. For topTable only, this defaults to fit$genes.
eb	subset of fit containing Empirical Bayesian estimates, so columns: 't', 'p-value' and 'lods' by default. For expert use only.
adjust.method	method used to adjust the p-values for multiple testing. Options, in increasing conservatism, include "none", "BH", "BY" and "holm". See p.adjust for the complete list of options. A NULL value will result in the default adjustment method, which is "BH".
sort.by	character string specifying which statistic to rank the genes by. Possible values for topTable are "logFC", "AveExpr", "t", "P", "p", "B" or "none". (Permitted synonyms are "M" for "logFC", "A" or "Amean" for "AveExpr", "T" for "t" and "p" for "P".) Possible values for topTableF are "F" or "none". topTreat accepts the same values as topTable except for "B".
resort.by	character string specifying statistic to sort the selected genes by in the output data.frame. Possibilities are the same as for sort.by.
p.value	cutoff value for adjusted p-values. Only genes with lower p-values are listed.
lfc	minimum absolute log2-fold-change required. topTable and topTableF include only genes with (at least one) absolute log-fold-change greater than lfc. topTreat does not remove genes but ranks genes by evidence that their log-fold-change exceeds lfc.

Methods

glmnet

fit = "glmnet", n = "numeric"

glmnet objects are produced by lassoClass or lassoReg

limma

fit = "limma", n = "numeric"

limma objects are produced by limma2Groups

MarrayLM

fit = "limma", n = "numeric"

MarrayLM objects are produced by lmFit of the limma package

pamClass

fit = "pamClass", n = "numeric"

pamClass objects are produced by pamClass

rfClass

fit = "rfClass", n = "numeric"

rfClass objects are produced by rfClass

tTest

fit = "tTest", n = "numeric"

tTest objects are produced by tTest

fTest

fit = "fTest", n = "numeric"

fTest objects are produced by fTest

See Also

• topTable-methods for: glmnet, lognet and elnet

• topTable,pamClass-method

• topTable,rfClass-method

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.