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
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: ", ...)
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 |
a list of Gviz tracks, invisibly returned
The Bioconductor workflow on cloud-enabled cis-eQTL analysis.