FunciSNPplot {FunciSNP} | R Documentation |
FunciSNPplot is a function developed to plot various types of plots to summarize and assist end-user in making informed discoveries of FunciSNP results. Plots can be stored in a folder for future reference.
FunciSNPplot(dat, rsq = 0, split = FALSE, splitbysnp = FALSE, tagSummary = FALSE, heatmap = FALSE, heatmap.key = FALSE,genomicSum = FALSE, save = FALSE, pathplot=getwd(), text.size=10, save.width=7, save.height=7)
dat |
FunciSNP data.frame: |
rsq |
an interger (0-1): |
split |
logical: |
splitbysnp |
logical: |
tagSummary |
logical: |
heatmap |
logical: |
heatmap.key |
logical: |
genomicSum |
logical: |
save |
logical: |
pathplot |
a character: |
text.size |
Text size passed to graphing functions |
save.width |
Width of saved images in inches |
save.height |
Height of saved images in inches |
NA
Plots are generated either in X11 or in specified folder.
NA
Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)
SG. Coetzee, SK. Rhie, BP. Berman, GA. Coetzee and H. Noushmehr, FunciSNP: An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs., Nucleic Acids Research, In press, 2012 (doi:10.1093/nar/gks542).
getFSNPs
, FunciSNPplot
, FunciSNPAnnotateSummary
, FunciSNPtable
, FunciSNPbed
data(glioma) gl <- FunciSNPAnnotateSummary(glioma) FunciSNPplot(gl) FunciSNPplot(gl, rsq=0, genomicSum=TRUE, save=FALSE) FunciSNPplot(gl, rsq=0.5, genomicSum=TRUE, save=FALSE) # DO NOT RUN #FunciSNPplot(gl, tagSummary=TRUE, rsq=0.5) #