Evaluate Gene Set Analysis with Pinnacle

Perform Gene Set Analysis (GSA) by comparing t-statistics from a given gene set to genome-wide t-statistics, while accounting for co-expression structure

Usage

pinnacle(
  fit,
  coef,
  geneSets,
  data,
  formula = ~1,
  setSize = c(10, 5000),
  quiet = FALSE,
  ...
)

Arguments

fit

regression model fit by limma::lmFit() or variancePartition::dream()

coef

indicate coefficient or contrast to be extracted from fit using topTable

geneSets

GeneSetCollection from GSEABase

data

data.frame storing properties of each gene, with rownames being gene names

formula

formula specifying covariates in regression using t-statistics as response

setSize

array of two elements specifying the min and max number of genes allowed in a gene set. Only gene sets satisfying these criteria are retained

quiet

suppresss messages

...

other arguments passed to lm_each_eclairs() and then lm

Value

data.frame with results for each gene set

Details

Examples