plotPinnacleResult: Plot panels of results

Description Usage Arguments

Description

Plot density of test statistics, pinnacle results and correlation within geneset

Usage

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plotPinnacleResult(vobj, fit, L, coef, corrStruct, geneSet, target,
  peakLocation, df_peakGeneMap, rank = ncol(vobj), decay = 0.00016)

Arguments

vobj

voom object

fit

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

L

contrast matrix

coef

coefficient

corrStruct

object from evalCorrelationDecomp() storing SVD of covariance matrix

geneSet

a single gene set

target

GRanges object of locations of genes

peakLocation

GRanges object of intervals measured in vobj

df_peakGeneMap

distances from each peak to genes from getPeakGeneDistances()

rank

of decomposition to bet set by truncating trailing eigen values

decay

weight function parameter


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