FunciSNPplot: FunciSNPplot to visualize YAFSNP summary.

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Description

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.

Usage

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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)

Arguments

dat

FunciSNP data.frame: dat is a data.frame object from FunciSNPAnnotateSummary. Need to run FunciSNPAnnotateSummary first.

rsq

an interger (0-1): rsq is the Rsquared cutoff used to subset.

split

logical: split will generate distribution plot of all Correlated SNPs by Rsquare values.

splitbysnp

logical: splitbysnp is similar to split but instead split the distribution by tagSNP.

tagSummary

logical: tagSummary Will output two plots per biofeature. The first one is a scatter plot showing the relationship between Rsquare and Distance to tagSNP for each YAFSNP. The second plot is a histogram distribution of number of correlated SNPs at each Rsquare value. Each set of plot is further divided by tagSNP. Best if used with rsq value.

heatmap

logical: heatmap correlation heatmap to visualize the number of correlated SNPs at each tagSNP overlapping each biological feature. Most informative if used with a rsq value.

heatmap.key

logical: heatmap.key Places the count of each cell on the heatmap.

genomicSum

logical: genomicSum Stacked bar chart summarizing all correlated SNPs for each of the identified genomie features (exon, intron, 5'UTR, 3'UTR, promoter, lincRNA or in gene desert (intergentic)). Most informative if used with a rsq value.

save

logical: save to save outputs to folder. Set at getwd(), in folder 'FunciSNP.VERSION/plots

pathplot

a character: pathplot is the path to the folder where to save the plots. Default to getwd() or current working directory.

text.size

Text size passed to graphing functions

save.width

Width of saved images in inches

save.height

Height of saved images in inches

Details

NA

Value

Plots are generated either in X11 or in specified folder.

Note

NA

Author(s)

Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)

References

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).

See Also

getFSNPs, FunciSNPplot, FunciSNPAnnotateSummary, FunciSNPtable, FunciSNPbed

Examples

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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)
#

shraddhapai/FunciSNP documentation built on May 29, 2019, 9:26 p.m.