scoresCis {GGtools} | R Documentation

## 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.

[Package GGtools version 5.16.0 Index]