scoresCis: visualize a gene model with cis-eQTL association scores (-log...

In GGtools: software and data for analyses in genetics of gene expression

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.

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.