[BioC] CGHCall problems
Bernard North [guest]
guest at bioconductor.org
Tue Aug 6 18:12:05 CEST 2013
I am using CGHcall to segment and call aCGH copy number data.
My understanding is that the segmentation step of CGHcall is the same CBS method used in DNAcopy.
CGHcall has a function called "calls" which has segments as rows (defined as start probe to end probe) and columns for each sample with the elements being calls.
Given that DNAcopy has a different segmentation for each sample how is the segmentation in allcalls decided upon ?
Calls is run as allcalls<-data.frame(calls(result)) where result is the final CGHCall object as per the vignette
Also does CGHcall provide pvalues or qvalues to test if any regions are recurrently amplified or deleted over samples ?
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=C LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 CGHcall_2.18.0 snowfall_1.84-4 snow_0.3-12 CGHbase_1.18.0
 marray_1.36.0 impute_1.32.0 GEOquery_2.24.1 Biobase_2.18.0
 BiocGenerics_0.4.0 snapCGH_1.28.0 limma_3.14.4 DNAcopy_1.32.0
loaded via a namespace (and not attached):
 aCGH_1.36.0 affy_1.36.1 affyio_1.26.0
 annotate_1.36.0 AnnotationDbi_1.20.7 BiocInstaller_1.8.3
 cluster_1.14.3 DBI_0.2-7 genefilter_1.40.0
 GLAD_2.20.0 grid_2.15.2 IRanges_1.16.6
 lattice_0.20-10 MASS_7.3-22 multtest_2.14.0
 parallel_2.15.2 pixmap_0.4-11 preprocessCore_1.20.0
 RColorBrewer_1.0-5 RCurl_1.95-4.1 RSQLite_0.11.4
 splines_2.15.2 stats4_2.15.2 strucchange_1.4-7
 survival_2.36-14 tilingArray_1.36.0 vsn_3.26.0
 XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.4.0
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