toptable-method: Table of Top Genes from Linear Model Fit

In GabrielHoffman/variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments

Table of Top Genes from Linear Model Fit

Description

topTable generic

topTable generic MArrayLM

topTable generic MArrayLM2

Usage

topTable(
  fit,
  coef = NULL,
  number = 10,
  genelist = fit$genes,
  adjust.method = "BH",
  sort.by = "B",
  resort.by = NULL,
  p.value = 1,
  lfc = 0,
  confint = FALSE
)

## S4 method for signature 'MArrayLM'
topTable(
  fit,
  coef = NULL,
  number = 10,
  genelist = fit$genes,
  adjust.method = "BH",
  sort.by = "p",
  resort.by = NULL,
  p.value = 1,
  lfc = 0,
  confint = FALSE
)

## S4 method for signature 'MArrayLM2'
topTable(
  fit,
  coef = NULL,
  number = 10,
  genelist = fit$genes,
  adjust.method = "BH",
  sort.by = "p",
  resort.by = NULL,
  p.value = 1,
  lfc = 0,
  confint = FALSE
)

Arguments

fit	fit
coef	coef
number	number
genelist	genelist
adjust.method	adjust.method
sort.by	sort.by
resort.by	resort.by
p.value	p.value
lfc	lfc
confint	confint

Value

results of toptable

results of toptable

results of toptable

GabrielHoffman/variancePartition documentation built on Nov. 8, 2024, 11:17 a.m.