Ringo/Starr genomeAnno Object Tips
0
0
Entering edit mode
Noah Dowell ▴ 410
@noah-dowell-3791
Last seen 8.1 years ago
Dear Benedikt, Thank you for your help in getting me up to speed with the Starr package. I want to provide you with some suggestions for vignette updates and post this to the Bioconductor board in case other people run into similar problems. 1. The probeAnno object created by the bpmapToProbeAnno function is slightly more complex when using the bpmap provided by Affymetrix (as opposed to the example bpmap in the vignette). a. All of the Affymetrix control probes are mapped (as chromosomes) but ignoring them has not caused any errors for me, just much larger file sizes. b. The nomenclature used for the "chromosomes" is not as simple as the nomenclature presented in the Ringo and Starr vignette. For example, users should use: Sc:Oct_2003;chr1 to name chromosome 1 in their genome annotation file. Maybe the chr1 naming convention is specific to Nimblgen. 2. Creating the genome Annotation object with BioMart is a good suggestion, but several things must also be matched up to get the genomeAnno object to look like the example tssAnno and to communicate with the probeAnno object. a. Change the chromosome names in the genomeAnno object as stated above. b. Rename and reorder the columns in the genomeAnno object to match the tssAnno object in the vignette c. The class of the elements in each column of the genomeAnno object must match that of the tssAnno. Things may get changed when they are being shuffled around. Below is what I used to change my classes, but I guess the getProfiles code could be rewritten slightly to throw an error in the beginning if it detects the wrong class in the genomeAnno object. geneAnno$chr <- as.character(geneAnno$chr) geneAnno$start <- as.integer(as.character(geneAnno$start)) geneAnno$end <- as.integer(as.character(geneAnno$end)) geneAnno$strand <- as.numeric(as.character(geneAnno$strand)) geneAnno$name <- as.character(geneAnno$name) Hope this is helpful. Best, Noah > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] Starr_1.2.0 affxparser_1.18.0 affy_1.24.0 Ringo_1.10.0 Matrix_0.999375-31 [6] lattice_0.17-26 limma_3.2.1 RColorBrewer_1.0-2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.0 DBI_0.2-4 [5] genefilter_1.28.0 MASS_7.3-3 preprocessCore_1.8.0 pspline_1.0-13 [9] RSQLite_0.7-3 splines_2.10.0 survival_2.35-7 tools_2.10.0 [13] xtable_1.5-5 [[alternative HTML version deleted]]
Annotation biomaRt Ringo Annotation biomaRt Ringo • 785 views