pinnacle: Evaluate gene set enrichments with Pinnacle

Description Usage Arguments Value Author(s)

Description

Enrichment analysis and hypothesis testing by comparing t-statistics from a given gene set to genome-wide t-statistics. Evaluated with pinnacle linear mixed model with either local or global correlation structure.

Gene set enrichment analysis based on genomic intervals from ChIP-seq, ATAC-seq, etc.

Usage

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pinnacle(vobj, fit, L, corrStruct, geneSets, target, rank = ncol(vobj),
  varianceFraction = 0.99, decay = 0.00016, squaredCorr = TRUE,
  quiet = FALSE)

Arguments

vobj

voom object

fit

model fit from lmFit() in limma or dream() in variancePartition

L

contrast matrix

corrStruct

object from evalCorrelationDecomp() storing SVD of covariance matrix

geneSets

list of genesets

target

GRanges object of locations of genes

rank

of decomposition to bet set by truncating trailing eigen values

varianceFraction

fraction of variance to retain after truncating trailing eigen values

decay

weight function parameter

squaredCorr

Compute decomposition of squared correlation for two-sided test

quiet

suppress messages

Value

table of enrichment statistics

Author(s)

Gabriel E. Hoffman


GabrielHoffman/pinnacle documentation built on May 3, 2019, 3:02 p.m.