hlatools provides a collection of tools to work with
IPD-IMGT/HLA data
Install from GitHub using remotes:
remotes::install_github("gschofl/hlatools")-
clone_IMGTHLA(): Clone the ANHIG/IMGTHLA repo on GitHub to a location specified by the optionhlatools.local_repos. Defaults to ~/local/db/. -
pull_IMGTHLA(): Send a pull request to ANHIG/IMGTHLA. -
check_IMGTHLA(): Check if your local repository is up-to-date.
A HLA gene can be read into a HLAGene object:
x <- hlatools::HLAGene("DPB1")
x
#> IPD-IMGT/HLA database <3.41.0>; Locus <HLA-DPB1>
#> An object of class 'HLAAllele' for 'HLA-DPB1'
#> DataFrame with 1584 rows and 6 columns
#> allele_name g_group p_group cwd_status SeqLen
#> <character> <character> <character> <character> <integer>
#> 1 HLA-DPB1*01:01:01:01 DPB1*01:01:01G DPB1*01:01P Common 11468
#> 2 HLA-DPB1*01:01:01:02 DPB1*01:01:01G DPB1*01:01P Not CWD defined 11468
#> 3 HLA-DPB1*01:01:01:03 DPB1*01:01:01G DPB1*01:01P Not CWD defined 11468
#> 4 HLA-DPB1*01:01:01:04 DPB1*01:01:01G DPB1*01:01P Not CWD defined 11468
#> 5 HLA-DPB1*01:01:01:05 DPB1*01:01:01G DPB1*01:01P Not CWD defined 11030
#> ... ... ... ... ... ...
#> 1580 HLA-DPB1*1116:01 None None Not CWD defined 677
#> 1581 HLA-DPB1*1117:01 DPB1*05:01:01G DPB1*05:01P Not CWD defined 677
#> 1582 HLA-DPB1*1118:01 DPB1*05:01:01G DPB1*05:01P Not CWD defined 657
#> 1583 HLA-DPB1*1119:01 DPB1*05:01:01G DPB1*05:01P Not CWD defined 657
#> 1584 HLA-DPB1*1120:01 DPB1*05:01:01G DPB1*05:01P Not CWD defined 657
#> FeatureType
#> <character>
#> 1 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 2 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 3 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 4 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 5 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> ... ...
#> 1580 Exon:Exon:Exon:Exon
#> 1581 Exon:Exon:Exon:Exon
#> 1582 Exon:Exon:Exon
#> 1583 Exon:Exon:Exon
#> 1584 Exon:Exon:ExonA number of accessor functions can be used to work with these objects:
x <- hlatools::HLAGene("DPA1")
hlatools::db_version(x)
#> [1] '3.41.0'
hlatools::locusname(x)
#> [1] "HLA-DPA1"
x1 <- x[hlatools::is_complete(x)][1:10]
hlatools::allele_name(x1)
#> [1] "HLA-DPA1*01:03:01:01" "HLA-DPA1*01:03:01:02" "HLA-DPA1*01:03:01:03"
#> [4] "HLA-DPA1*01:03:01:04" "HLA-DPA1*01:03:01:05" "HLA-DPA1*01:03:01:06"
#> [7] "HLA-DPA1*01:03:01:07" "HLA-DPA1*01:03:01:08" "HLA-DPA1*01:03:01:09"
#> [10] "HLA-DPA1*01:03:01:10"
hlatools::cwd_status(x1)
#> [1] "Common" "Not CWD defined" "Not CWD defined" "Not CWD defined"
#> [5] "Not CWD defined" "Not CWD defined" "Not CWD defined" "Not CWD defined"
#> [9] "Not CWD defined" "Not CWD defined"
hlatools::ethnicity(x1)
#> [1] "Caucasoid:Oriental" "Caucasoid:Black" "Caucasoid"
#> [4] "Caucasoid" "Caucasoid" "Oriental"
#> [7] "Oriental" "Oriental" "Caucasoid"
#> [10] "Caucasoid"
hlatools::g_group(x1)
#> [1] "DPA1*01:03:01G" "DPA1*01:03:01G" "DPA1*01:03:01G" "DPA1*01:03:01G"
#> [5] "DPA1*01:03:01G" "DPA1*01:03:01G" "DPA1*01:03:01G" "DPA1*01:03:01G"
#> [9] "DPA1*01:03:01G" "DPA1*01:03:01G"
hlatools::p_group(x1)
#> [1] "DPA1*01:03P" "DPA1*01:03P" "DPA1*01:03P" "DPA1*01:03P" "DPA1*01:03P"
#> [6] "DPA1*01:03P" "DPA1*01:03P" "DPA1*01:03P" "DPA1*01:03P" "DPA1*01:03P"
hlatools::sequences(x1)
#> DNAStringSet object of length 10:
#> width seq names
#> [1] 9775 GGTGGACCTGAAAGAAAGATTAA...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:01
#> [2] 9775 GGTGGACCTGAAAGAAAGATTAA...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:02
#> [3] 9775 GGTGGACCTGAAAGAAAGATTAA...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:03
#> [4] 9775 GGTGGACCTGAAAGAAAGATTAA...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:04
#> [5] 9757 GGTGGACCTGAAAGAAAGATTAA...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:05
#> [6] 9479 AAATTCTCCCATCTCTTCCCCAG...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:06
#> [7] 9477 AAATTCTCCCATCTCTTCCCCAG...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:07
#> [8] 9478 AAATTCTCCCATCTCTTCCCCAG...AAAAAAGGAATTGTTTAAAGTA HLA-DPA1*01:03:01:08
#> [9] 5265 TTACCCAGCAACAGAGAATGTCA...CCGATAACTAACTGAGTAGTTA HLA-DPA1*01:03:01:09
#> [10] 5735 TTTTTACATCTCTTTCTCTAACT...GGTGGGTGCCTGTAACTACTTA HLA-DPA1*01:03:01:10
hlatools::exon(x1, exon = 2)
#> DNAStringSet object of length 10:
#> width seq names
#> [1] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [2] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [3] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [4] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [5] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [6] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [7] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [8] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [9] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...
#> [10] 246 CGGACCATGTGTCAACTTATGCC...AACCACACTCAGGCCACCAACG HLA-DPA1*01:03:01...We can access previous releases of the IPD-IMGT/HLA database:
x <- hlatools::HLAGene("DPB1", db_version = "3.25.0")
x
#> IPD-IMGT/HLA database <3.25.0>; Locus <HLA-DPB1>
#> An object of class 'HLAAllele' for 'HLA-DPB1'
#> DataFrame with 671 rows and 6 columns
#> allele_name g_group p_group cwd_status SeqLen
#> <character> <character> <character> <character> <integer>
#> 1 HLA-DPB1*01:01:01 Common 777
#> 2 HLA-DPB1*01:01:02 Common 777
#> 3 HLA-DPB1*01:01:03 Not CWD defined 264
#> 4 HLA-DPB1*01:01:04 Not CWD defined 264
#> 5 HLA-DPB1*01:01:05 Not CWD defined 264
#> ... ... ... ... ... ...
#> 667 HLA-DPB1*568:01 Not CWD defined 264
#> 668 HLA-DPB1*569:01 Not CWD defined 264
#> 669 HLA-DPB1*570:01N Not CWD defined 264
#> 670 HLA-DPB1*571:01 Not CWD defined 657
#> 671 HLA-DPB1*572:01 Not CWD defined 546
#> FeatureType
#> <character>
#> 1 Exon:Exon:Exon:Exon:Exon
#> 2 Exon:Exon:Exon:Exon:Exon
#> 3 Exon
#> 4 Exon
#> 5 Exon
#> ... ...
#> 667 Exon
#> 668 Exon
#> 669 Exon
#> 670 Exon:Exon:Exon
#> 671 Exon:Exon
hlatools::db_version(x)
#> [1] '3.25.0'
hlatools::locusname(x)
#> [1] "HLA-DPB1"
x[hlatools::cwd_status(x) == "Common"][1:10]
#> An object of class 'HLAAllele' for 'HLA-DPB1'
#> DataFrame with 10 rows and 6 columns
#> allele_name g_group p_group cwd_status SeqLen
#> <character> <character> <character> <character> <integer>
#> 1 HLA-DPB1*01:01:01 Common 777
#> 2 HLA-DPB1*01:01:02 Common 777
#> 3 HLA-DPB1*02:01:02 Common 11532
#> 4 HLA-DPB1*02:02 Common 11528
#> 5 HLA-DPB1*03:01:01 Common 11461
#> 6 HLA-DPB1*04:01:01:01 Common 11526
#> 7 HLA-DPB1*04:02:01:01 Common 11516
#> 8 HLA-DPB1*05:01:01 Common 777
#> 9 HLA-DPB1*06:01:01 Common 777
#> 10 HLA-DPB1*09:01:01 Common 777
#> FeatureType
#> <character>
#> 1 Exon:Exon:Exon:Exon:Exon
#> 2 Exon:Exon:Exon:Exon:Exon
#> 3 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 4 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 5 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 6 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 7 UTR:Exon:Intron:Exon:Intron:Exon:Intron:Exon:Intron:Exon:UTR
#> 8 Exon:Exon:Exon:Exon:Exon
#> 9 Exon:Exon:Exon:Exon:Exon
#> 10 Exon:Exon:Exon:Exon:ExonThese objects come with an additional set of R6-methods that implement
an API used mostly in conjunction with the DR2S package:
-
x$get_closest_complete_neighbor(allele, partially = TRUE): Find the closest full-length allele based on the genetic distance between exon sequences. -
x$get_reference_sequence(allele): Return aBStringSetobject of a full-length reference sequence forallele. Ifalleleis not fully known the missing stretches are taken from the allele returned by a call toget_closest_complete_neighbor().
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