hlaLociInfo: HLA/KIR Locus Information

In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description

To get the starting and ending positions in basepair of HLA/KIR loci.

Usage

hlaLociInfo(assembly=c("auto", "auto-silent", "hg18", "hg19", "hg38",
    "unknown"))

Arguments

assembly

the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

Value

Return a data frame include the genomic locations.

Author(s)

Xiuwen Zheng

References

GeneCards: https://www.genecards.org/cgi-bin/carddisp.pl?gene=, NCBI Resources: http://www.ncbi.nlm.nih.gov/gene, HLA Nomenclature: http://hla.alleles.org/genes/index.html

Examples

hlaLociInfo()

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.3
Supported by Streaming SIMD Extensions (SSE2) [64-bit]
using the default genome assembly (assembly="hg19")
       chrom    start      end
MHC        6 29719561 32883508
A          6 29910247 29913661
B          6 31321649 31324989
C          6 31236526 31239913
E          6 30457183 30461982
F          6 29691117 29695073
G          6 29794756 29798899
H          6 29855383 29858856
J          6 29973748 29977733
K          6 29894436 29897616
L          6 30227339 30234728
N          6 30318851 30319815
P          6 29767821 29770856
S          6 31349346 31350264
T          6 29864220 29866724
U          6 29901541 29902657
V          6 29759530 29760527
W          6 29923611 29926835
X          6 31429623 31430267
Z          6 32864179 32864266
C4A        6 31949834 31970457
C4B        6 31982572 32003195
DMA        6 32916391 32920900
DMB        6 32902406 32908847
DOA        6 32971959 32977389
DOB        6 32780540 32784825
DRA        6 32407619 32412823
DRB1       6 32546546 32557613
DRB3       6  3715358  3728445
DRB4       6  3882321  3897284
DRB5       6 32485151 32498006
DQA1       6 32605169 32612152
DQA2       6 32709156 32714664
DQB1       6 32627241 32634466
DQB2       6 32723837 32731330
DPA1       6 33032346 33048555
DPA2       6 33059259 33061091
DPA3       6 33098974 33099120
DPB1       6 33043703 33057473
DPB2       6 33080293 33096890
MICA       6 31367561 31383090
MICB       6 31462054 31478901
MICC       6 30382490 30387543
MICD       6 29938149 29943522
MICE       6 29709234 29716880
HSPA1A     6 31782952 31785719
HSPA1B     6 31789964 31798032
HSPA1L     6 31777396 31790093
LTA        6 31539876 31542101
LTB        6 31548335 31550202
PSMB8      6 32808494 32812712
PSMB9      6 32821927 32827628
TAP1       6 32812986 32821748
TAP2       6 32789610 32806547
TNF        6 31543344 31546113

HIBAG documentation built on March 24, 2021, 6 p.m.