missing region in the process of annotation
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12 weeks ago
Aki ▴ 10

Hi. I am analyzing TCGA methylation data from TCGAbiolinks and I faced one problem during annotation process with annotatr. This TCGA data has covered a gene in the chromosome 19, but annotated result did not contain one region in chromosome 19. I used the opensea region probe for compartment analysis and there is no opensea probe for these genes in missing region. The genes are covered by only Island, N_Shore, and S_Shore region probe. Is that because, I couldn't observe the annotation result of the gene? I used following script. Thank you for your help.

library(minfi)
compartments_result <- compartments(GRset, chr = paste0("chr", 19), what = "OpenSea", resolution = 100 * 1000)

library(annotatr)
annots = 'hg19_basicgenes'
annotations = build_annotations(genome = 'hg19', annotations = annots)

AB_annotated_results <- annotate_regions(regions = compartments_result,
                                         annotations = annotations,
                                         ignore.strand = TRUE,
                                         quiet = FALSE)
annotatr minfi • 171 views
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