MetaQC (version 0.1.13)

plot.proto: Plot MetaQC results.

Description

It draws a PCA biplot which shows the four QC measures. CQCg and AQCg are combined to be CAQCg, and CQCp and AQCp are combined to be CAQCp to reduce the dominance of CQC and AQC due to their greater correlation.

Usage

"plot"(x, ...)

Arguments

x

A proto R object which obtained by MetaQC function.

...

Further arguments to print function.

Value

NA

References

Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng. (Nucleic Acids Res. 2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis.

See Also

MetaQC

Examples

## Not run: 
#     requireAll(c("proto", "foreach"))
# 
#    ## Toy Example
#     data(brain) #already hugely filtered
#     #Two default gmt files are automatically downloaded, 
# 	#otherwise it is required to locate it correctly.
#     #Refer to http://www.broadinstitute.org/gsea/downloads.jsp
#     brainQC <- MetaQC(brain, "c2.cp.biocarta.v3.0.symbols.gmt", 
# 						filterGenes=FALSE, verbose=TRUE)
# 	#B is recommended to be >= 1e4 in real application					
#     runQC(brainQC, B=1e2, fileForCQCp="c2.all.v3.0.symbols.gmt")
#     plot(brainQC)
# 
# ## End(Not run)