get_top_table: Get top table

In alexvpickering/crossmeta: Cross Platform Meta-Analysis of Microarray Data

Get top table

Description

Get top table

Usage

get_top_table(
  lm_fit,
  groups = c("test", "ctrl"),
  with.es = TRUE,
  robust = FALSE,
  trend = FALSE,
  allow.no.resid = FALSE
)

Arguments

lm_fit	Result of run_limma
groups	Test and Control group as strings.
with.es	Add 'dprime' and 'vardprime' from effectsize? Default is TRUE.
robust	logical, should the estimation of df.prior and var.prior be robustified against outlier sample variances?
trend	logical, should an intensity-dependent trend be allowed for the prior variance? If FALSE then the prior variance is constant. Alternatively, trend can be a row-wise numeric vector, which will be used as the covariate for the prior variance.
allow.no.resid	Allow no residual degrees of freedom? if TRUE and the fit contrast matrix has no residual degrees of freedom, eBayes fit is skipped and the result of contrasts.fit is returned.

Value

result of toptable

alexvpickering/crossmeta documentation built on June 2, 2022, 7:06 a.m.