GGtools (version 5.8.0)

scoresCis: visualize a gene model with cis-eQTL association scores (-log FDR by default) on the basis of a ciseqByCluster data.table output

Description

visualize a gene model with cis-eQTL association scores (-log FDR by default) on the basis of a ciseqByCluster data.table output

Usage

scoresCis(sym = "ORMDL3", cisRun, 
   cisannopk = "lumiHumanAll.db", radius = 1e+05, pad = 1000, 
   txScore = function(x) -log10(x + (1e-05)), ylim = c(0, 4), 
   genometag = "hg19", plot.it = TRUE, laxistag = "-log10 FDR: ", ...)

Arguments

sym

gene symbol to be resolved into probe id using cisannopk

cisRun

data.table output of ciseqByCluster

cisannopk

Annotation resource, often a ChipDb instance

radius

radius to be added to gene model for display, should typically agree with that used in the search

pad

some extra space

txScore

function that will transform fdr for rendering

ylim

vertical limits for fdr display

genometag

coordinates from this build of genome

plot.it

logical dictating whether plotTracks will be run

laxistag

token used to tell what units are used on vertical axis

...

not used

Value

• a list of Gviz tracks, invisibly returned

See Also

The Bioconductor workflow on cloud-enabled cis-eQTL analysis.