The liftOver facilities developed in conjunction with the UCSC browser track infrastructure are available for transforming data in GRanges formats. This is illustrated here with an image of the EBI/NHGRI GWAS catalog that is, as of May 10 2017, distributed with coordinates defined by NCBI build hg38.
R version: R version 4.4.1 (2024-06-14)
Bioconductor version: 3.20
Package version: 1.30.0
library(gwascat)
cur = makeCurrentGwascat() # result varies by daydata(cur)
cur## gwasloc instance with 65795 records and 37 attributes per record.
## Extracted: 2018-04-24
## Genome: GRCh38 NA
## Excerpt:
## GRanges object with 5 ranges and 3 metadata columns:
## seqnames ranges strand | DISEASE/TRAIT SNPS P-VALUE
## <Rle> <IRanges> <Rle> | <character> <character> <numeric>
## [1] 17 78284479 * | Inflammatory skin di.. rs9302874 2e-07
## [2] 10 129683009 * | Inflammatory skin di.. rs80312298 6e-07
## [3] 1 247490110 * | Inflammatory skin di.. rs10802516 6e-06
## [4] 2 60845432 * | Inflammatory skin di.. rs35741374 4e-12
## [5] 1 152619805 * | Inflammatory skin di.. rs1581803 2e-12
## -------
## seqinfo: 24 sequences from 2 genomes (GRCh38, NA)The transformation to hg19 coordinates is defined by a chain file provided by UCSC. rtracklayer::import.chain will bring the data into R.
library(rtracklayer)
path = system.file(package="liftOver", "extdata", "hg38ToHg19.over.chain")
ch = import.chain(path)
ch## Chain of length 25
## names(25): chr22 chr21 chr19 chr20 chrY chr18 ... chr6 chr5 chr4 chr3 chr2 chr1str(ch[[1]])## Formal class 'ChainBlock' [package "rtracklayer"] with 6 slots
## ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
## .. .. ..@ start : int [1:6842] 16367189 16386933 16386970 16387001 16387128 16395491 16395528 16395841 16395860 16395956 ...
## .. .. ..@ width : int [1:6842] 19744 36 31 112 8362 36 312 18 95 33 ...
## .. .. ..@ NAMES : NULL
## .. .. ..@ elementType : chr "ANY"
## .. .. ..@ elementMetadata: NULL
## .. .. ..@ metadata : list()
## ..@ offset : int [1:6842] -480662 -480702 -480702 -480726 -480726 -480726 -480726 -480726 -480726 -480726 ...
## ..@ score : int [1:1168] -1063867308 68830488 21156147 20814926 7358950 3927744 2928210 991419 880681 802146 ...
## ..@ space : chr [1:1168] "chr22" "chr14" "chr22" "chr21" ...
## ..@ reversed: logi [1:1168] FALSE FALSE FALSE FALSE FALSE FALSE ...
## ..@ length : int [1:1168] 1124 1280 173 465 398 110 43 173 342 84 ...Some more details about the chain data structure are available in the import.chain man page
A chain file essentially details many local alignments, so it is possible for the "from" ranges to map to overlapping regions in the other sequence. The "from" ranges are guaranteed to be disjoint (but do not necessarily cover the entire "from" sequence).
The liftOver function will create a GRangesList.
seqlevelsStyle(cur) = "UCSC" # necessary
cur19 = liftOver(cur, ch)
class(cur19)## [1] "CompressedGRangesList"
## attr(,"package")
## [1] "GenomicRanges"We unlist and coerce to the gwaswloc class, a convenient form for the GWAS catalog with its many mcols fields.
cur19 = unlist(cur19)
genome(cur19) = "hg19"
cur19 = new("gwaswloc", cur19)
cur19## gwasloc instance with 65757 records and 37 attributes per record.
## Extracted:
## Genome: hg19
## Excerpt:
## GRanges object with 5 ranges and 3 metadata columns:
## seqnames ranges strand | DISEASE/TRAIT SNPS P-VALUE
## <Rle> <IRanges> <Rle> | <character> <character> <numeric>
## [1] chr17 76280560 * | Inflammatory skin di.. rs9302874 2e-07
## [2] chr10 131481273 * | Inflammatory skin di.. rs80312298 6e-07
## [3] chr1 247653412 * | Inflammatory skin di.. rs10802516 6e-06
## [4] chr2 61072567 * | Inflammatory skin di.. rs35741374 4e-12
## [5] chr1 152592281 * | Inflammatory skin di.. rs1581803 2e-12
## -------
## seqinfo: 24 sequences from hg19 genome; no seqlengthsWe see that the translation leads to a loss of some loci.
length(cur)-length(cur19)## [1] 38setdiff(mcols(cur)$SNPS, mcols(cur19)$SNPS)## [1] "rs757210" "rs8064454" "rs386000" "rs644148" "rs9876781"
## [6] "rs1167796" "rs649129" "rs11672691" "rs4911642" "rs718433"
## [11] "rs138700403" "rs144184641" "rs147767607" "rs148916504" "rs149506335"
## [16] "rs192514996" "rs2734221" "rs2855983" "rs4457242" "rs7777677"
## [21] "rs201386833" "rs3757378" "rs400942" "rs11263761" "rs8176645"
## [26] "rs11785400" "rs451000" "rs450937" "rs12601991" "rs7256693"
## [31] "rs3020736" "rs453755"It may be interesting to follow up some of the losses.