aa_granges: Convert tumor amino acid ranges to a GRanges object

In cancer-genomics/trellis: Somatic structural variant analysis

Convert tumor amino acid ranges to a GRanges object

Description

Convert tabled amino acid ranges to a GRanges object to facilitate the overlap with protein domains from Uniprot database.

Usage

aa_granges(tab)

Arguments

tab	a DataFrame of fusions as obtained from fusionTable2

Examples

 extdata <- system.file("extdata", package="svbams")
 fusions <- readRDS(file.path(extdata, "valid_fusions.rds"))
 tab <- fusionTable2(fusions)
 extdata2 <- system.file("extdata", package="svbams")
 up <- readRDS(file.path(extdata2, "uniprot.rds"))
 up2 <- uniprotFeatures(up, tab, strwrap.width=20)
 ## check that none of the short descriptions are too long
 nchar.desc <- nchar(up2$short.desc)
 gene1.in.up <- tab$gene.5prime %in% up2$hugo
 gene2.in.up <- tab$gene.3prime %in% up2$hugo
 bothin.up <- gene1.in.up & gene2.in.up
 tab <- tab[bothin.up, ]
 ## the aa_len field of the amino acid in uniprot might have a zero-based index
 ## -- it is one smaller than the length we've recorded
 ## coerce to GRanges
 tumor_aa_ranges <- aa_granges(tab)
 identical(as.character(seqnames(tumor_aa_ranges)),
           rep(c("ERBB4", "IKZF2"), each=2))
 domain_aa_ranges <- GRanges(up2$hugo, IRanges(up2$start, up2$end),
                             chromosome=up2$seqnames,
                             description=up2$description,
                             short.desc=up2$short.desc,
                             aa_len=up2$aa_len)
 domains <- subsetByOverlaps(domain_aa_ranges, tumor_aa_ranges, type="within")
 domains

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.