hlaLociInfo: HLA Locus Information

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

Description

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

Usage

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

Arguments

assembly

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

Value

Return a list:

loci	the names of HLA classic I, II and III genes, such like A, B, C, DRB1, DQA1, DQB1 and DPB1
pos.HLA.start	the starting position in basepair
pos.HLA.end	the ending position in basepair
length.HLA	the length of HLA genes in basepair

Author(s)

Xiuwen Zheng

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 May 2, 2019, 4:50 p.m.