Description Usage Arguments Value Author(s) References See Also Examples
It prints out the results of all QC measures and standardized mean rank of each study. 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.
1 2 |
x |
A proto R object which obtained by MetaQC function. |
... |
Further arguments to print function. |
NA
Don Kang (donkang75@gmail.com) and George Tseng (ctseng@pitt.edu)
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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")
brainQC
## End(Not run)
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