fit_limma {autonomics}

R Documentation

Fit model and test for differential expression

Description

Fit model and test for differential expression

Usage

fit_limma(
  object,
  subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL,
  formula = default_formula(object, subgroupvar, "limma"),
  contrastdefs = contrast_coefs(object, formula),
  block = NULL,
  weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL,
  verbose = TRUE,
  plot = FALSE
)

fit_lm(
  object,
  subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL,
  formula = default_formula(object, subgroupvar, fit = "lm"),
  block = NULL,
  weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL,
  contrastdefs = NULL,
  verbose = TRUE,
  plot = FALSE
)

fit_lme(
  object,
  subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL,
  formula = default_formula(object, subgroupvar, fit = "lme"),
  block = NULL,
  weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL,
  contrastdefs = NULL,
  verbose = TRUE,
  plot = FALSE
)

fit_lmer(
  object,
  subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL,
  formula = default_formula(object, subgroupvar, fit = "lmer"),
  block = NULL,
  weightvar = if ("weights" %in% assayNames(object)) "weights" else NULL,
  contrastdefs = NULL,
  verbose = TRUE,
  plot = FALSE
)

fit_wilcoxon(
  object,
  subgroupvar = if ("subgroup" %in% svars(object)) "subgroup" else NULL,
  formula = default_formula(object, subgroupvar, fit = "wilcoxon"),
  contrastdefs = contrast_coefs(object, formula = formula),
  block = NULL,
  weightvar = NULL,
  verbose = TRUE,
  plot = FALSE
)

Arguments

object	SummarizedExperiment
subgroupvar	subgroup variable
formula	modeling formula
contrastdefs	contrastdef vector / matrix / list c("t1-t0", "t2-t1", "t3-t2") matrix(c("WT.t1-WT.t0", "WT.t2-WT.t1", "WT.t3-WT.t2"), c("KD.t1-KD.t0", "KD.t2-KD.t1", "KD.t3-KD.t2"), nrow=2, byrow=TRUE) list(matrix(c("WT.t1-WT.t0", "WT.t2-WT.t1", "WT.t3-WT.t2"), c("KD.t1-KD.t0", "KD.t2-KD.t1", "KD.t3-KD.t2"), nrow=2, byrow=TRUE), matrix(c("KD.t0-WT.t0", "KD.t1-WT.t1", "KD.t2-WT.t2", "KD.t3-WT.t3"), nrow=1, byrow=TRUE))
block	block svar (or NULL)
weightvar	NULL or name of weight matrix in assays(object)
verbose	whether to msg
plot	whether to plot

Value

Updated SummarizedExperiment

Examples

require(magrittr)
file <- download_data('atkin18.somascan.adat')
object <- read_somascan(file, plot=FALSE)
object %<>% fit_limma(subgroupvar = 'SampleGroup')
object %<>% fit_lm(   subgroupvar = 'SampleGroup')
plot_venn(is_sig(object, contrast='t3-t2'))

S4Vectors::metadata(object)$limma <- S4Vectors::metadata(object)$lm <- NULL
object %<>% fit_limma(   subgroupvar = 'SampleGroup', block = 'Subject_ID')
object %<>% fit_wilcoxon(subgroupvar = 'SampleGroup', block = 'Subject_ID')
# object %<>% fit_lme(   subgroupvar = 'SampleGroup', block = 'Subject_ID')
# object %<>% fit_lmer(  subgroupvar = 'SampleGroup', block = 'Subject_ID')
plot_venn(is_sig(object, contrast='t3-t2'))

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