How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)? Is there any package(s) that lets me convert the gene symbol to cytogenetic bands?
Organism.dplyr provides another fun option, exposing the org and TxDb databases as dplyr objects
> library(Organism.dplyr)
> src = src_ucsc("Human")
using org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene
> src
src: sqlite 3.19.3 [/home/mtmorgan/.cache/BiocFileCache/5b377bf41425_5b377bf41425]
tbls: id, id_accession, id_go, id_go_all, id_omim_pm, id_protein,
id_transcript, ranges_cds, ranges_exon, ranges_gene, ranges_tx
> tbl(src, "id") %>% filter(symbol %like% "BRCA%") %>% dplyr::select(map, symbol) %>% distinct()
# Source: lazy query [?? x 2]
# Database: sqlite 3.19.3
# [/home/mtmorgan/.cache/BiocFileCache/5b377bf41425_5b377bf41425]
map symbol
<chr> <chr>
1 5p12 BRCAT54
2 17q21.31 BRCA1P1
3 13q21 BRCA3
4 17q21.31 BRCA1
5 13q13.1 BRCA2
6 11q23 BRCATA
The biovizBase package has a GRanges of the hg19 cytogenetic bands, so you could use that. There is also a GRanges with gene symbols in that package which makes it super convenient. Let's say we want the cytoband for BRCA2:
> library(biovizBase)
> data(hg19IdeogramCyto)
> data(genesymbol)
> subsetByOverlaps(hg19IdeogramCyto, genesymbol["BRCA2",])
GRanges object with 1 range and 2 metadata columns:
seqnames ranges strand | name gieStain
<Rle> <IRanges> <Rle> | <factor> <factor>
[1] chr13 [32200000, 34000000] * | q13.1 gpos50
-------
seqinfo: 24 sequences from an unspecified genome; no seqlengths
So BRCA2 is in 13q13.1. Is that what you are after?
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version 2.3.6
I forgot about the MAP column. You can get this directly without having to engage with any of that tidyverse nonsense <shakes cane at kids on lawn>.