The annotate package provides a class that can be used to model
chromosomal information about a species, using one of the metadata
packages provided by Bioconductor. This class contains information about
the organism and its chromosomes and provides a standardized interface
to the information in the metadata packages for other software to
quickly extract necessary chromosomal information. An example of using
chromLocation objects in other software can be found with the
alongChrom function of the geneplotter package in Bioconductor.
The chromLocation class is used to provide a structure for chromosomal data of
a particular organism. In this section, we will discuss the various slots of the
class and the methods for interacting with them. Before this though, we will
create an object of class chromLocation for demonstration purposes later. The
helper function buildChromLocation is used, and it takes as an argument the
name of a Bioconductor metadata package, which is itself used to extract the
data. For this vignette, we will be using the hgu95av2.db
package.
library("annotate")
z <- buildChromLocation("hgu95av2")
z## Instance of a chromLocation class with the following fields:
## Organism: Homo sapiens
## Data source: hgu95av2
## Number of chromosomes for this organism: 711
## Chromosomes of this organism and their lengths in base pairs:
## 1 : 248956422
## 2 : 242193529
## 3 : 198295559
## 4 : 190214555
## 5 : 181538259
## 6 : 170805979
## 7 : 159345973
## X : 156040895
## 8 : 145138636
## 9 : 138394717
## 11 : 135086622
## 10 : 133797422
## 12 : 133275309
## 13 : 114364328
## 14 : 107043718
## 15 : 101991189
## 16 : 90338345
## 17 : 83257441
## 18 : 80373285
## 20 : 64444167
## 19 : 58617616
## Y : 57227415
## 22 : 50818468
## 21 : 46709983
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## 20_KI270869v1_alt : 118774
## 17_KZ559114v1_alt : 116753
## 21_GL383581v2_alt : 116689
## 4_MU273350v1_fix : 113364
## 3_KI270781v1_alt : 113034
## 17_KI270730v1_random : 112551
## Un_KI270438v1 : 112505
## 4_KI270787v1_alt : 111943
## 18_KI270864v1_alt : 111737
## 2_KI270771v1_alt : 110395
## 1_GL383519v1_alt : 110268
## 2_KI270768v1_alt : 110099
## 1_KI270760v1_alt : 109528
## 12_KQ090023v1_alt : 109323
## 3_KI270783v1_alt : 109187
## 11_KN196481v1_fix : 108875
## 17_KI270859v1_alt : 108763
## 8_MU273361v1_fix : 106905
## 11_KI270902v1_alt : 106711
## 3_KZ559104v1_fix : 105527
## 18_GL383568v1_alt : 104552
## 12_MU273372v1_fix : 104537
## 22_KI270737v1_random : 103838
## 13_KI270843v1_alt : 103832
## 8_KZ559107v1_alt : 103072
## 22_KI270877v1_alt : 101331
## 5_GL383530v1_alt : 101241
## Y_KN196487v1_fix : 101150
## 22_KQ759762v2_fix : 101040
## 22_KQ759762v1_fix : 101037
## 19_KV575257v1_alt : 100553
## 11_KI270721v1_random : 100316
## 19_KV575254v1_alt : 99845
## 22_KI270738v1_random : 99375
## 15_ML143369v1_fix : 97763
## 22_GL383583v2_alt : 96924
## 2_GL582966v2_alt : 96131
## Un_KI270748v1 : 93321
## 18_KZ208922v1_fix : 93070
## Un_KI270435v1 : 92983
## 5_GL000208v1_random : 92689
## Un_KI270538v1 : 91309
## 4_KQ090013v1_alt : 90922
## 17_GL383566v1_alt : 90219
## 5_ML143350v1_fix : 89956
## 16_GL383557v1_alt : 89672
## 19_MU273387v1_alt : 89211
## 17_JH159148v1_alt : 88070
## 16_MU273376v1_fix : 87715
## 12_KN538370v1_fix : 86533
## 10_KN538366v1_fix : 85284
## 2_ML143342v1_fix : 84043
## 5_GL383532v1_alt : 82728
## 21_KI270872v1_alt : 82692
## 6_KQ090017v1_alt : 82315
## Un_KI270756v1 : 79590
## 16_KZ208921v1_alt : 78609
## 6_KI270758v1_alt : 76752
## 12_KI270833v1_alt : 76061
## 6_KI270802v1_alt : 75005
## 21_GL383580v2_alt : 74653
## 22_KB663609v1_alt : 74013
## 22_KI270739v1_random : 73985
## 6_ML143351v1_fix : 73265
## 9_GL383540v1_alt : 71551
## Un_KI270757v1 : 71251
## 2_KI270773v1_alt : 70887
## 17_JH159147v1_alt : 70345
## X_MU273393v1_fix : 68810
## X_ML143383v1_fix : 68192
## 11_KI270827v1_alt : 67707
## 1_KI270709v1_random : 66860
## Un_KI270746v1 : 66486
## 13_ML143365v1_fix : 65394
## 12_KZ208917v1_fix : 64689
## 16_KI270856v1_alt : 63982
## 21_GL383578v2_alt : 63917
## Un_KI270753v1 : 62944
## 19_KI270868v1_alt : 61734
## 9_GL383542v1_alt : 60032
## 16_KQ090026v1_alt : 59016
## 20_KI270871v1_alt : 58661
## 17_ML143375v1_fix : 56695
## 12_KI270836v1_alt : 56134
## 4_ML143346v1_fix : 53476
## 19_KI270865v1_alt : 52969
## 1_KI270764v1_alt : 50258
## Y_KZ208923v1_fix : 48370
## 11_ML143356v1_fix : 45257
## 1_KZ559100v1_fix : 44955
## Un_KI270589v1 : 44474
## 14_KI270726v1_random : 43739
## 19_KI270866v1_alt : 43156
## 22_KI270735v1_random : 42811
## 1_KI270711v1_random : 42210
## Un_KI270745v1 : 41891
## 1_KI270714v1_random : 41717
## 22_KI270732v1_random : 41543
## 1_KI270713v1_random : 40745
## Un_KI270754v1 : 40191
## 1_KI270710v1_random : 40176
## 12_KI270837v1_alt : 40090
## 9_KI270717v1_random : 40062
## 14_KI270724v1_random : 39555
## 8_MU273360v1_fix : 39290
## 9_KI270720v1_random : 39050
## 14_KI270723v1_random : 38115
## 9_KI270718v1_random : 38054
## Un_KI270317v1 : 37690
## 13_KI270842v1_alt : 37287
## Y_KI270740v1_random : 37240
## Un_KI270755v1 : 36723
## 8_KI270820v1_alt : 36640
## 13_KN196483v1_fix : 35455
## 5_MU273352v1_fix : 34400
## 1_KI270707v1_random : 32032
## Un_KI270579v1 : 31033
## X_ML143382v1_fix : 28824
## Un_KI270752v1 : 27745
## 9_ML143353v1_fix : 25408
## Un_KI270512v1 : 22689
## Un_KI270322v1 : 21476
## X_ML143385v1_fix : 17435
## M : 16569
## Un_GL000226v1 : 15008
## X_ML143384v1_fix : 14678
## 10_KN538365v1_fix : 14347
## Un_KI270311v1 : 12399
## 22_ML143379v1_fix : 12295
## Un_KI270366v1 : 8320
## Un_KI270511v1 : 8127
## Un_KI270448v1 : 7992
## Un_KI270521v1 : 7642
## 13_ML143363v1_fix : 7309
## Un_KI270581v1 : 7046
## Un_KI270582v1 : 6504
## Un_KI270515v1 : 6361
## Un_KI270588v1 : 6158
## Un_KI270591v1 : 5796
## Un_KI270522v1 : 5674
## Un_KI270507v1 : 5353
## Un_KI270590v1 : 4685
## Un_KI270584v1 : 4513
## Un_KI270320v1 : 4416
## Un_KI270382v1 : 4215
## Un_KI270468v1 : 4055
## Un_KI270467v1 : 3920
## Un_KI270362v1 : 3530
## Un_KI270517v1 : 3253
## Un_KI270593v1 : 3041
## Un_KI270528v1 : 2983
## Un_KI270587v1 : 2969
## Un_KI270364v1 : 2855
## Un_KI270371v1 : 2805
## Un_KI270333v1 : 2699
## Un_KI270374v1 : 2656
## Un_KI270411v1 : 2646
## Un_KI270414v1 : 2489
## Un_KI270510v1 : 2415
## Un_KI270390v1 : 2387
## Un_KI270375v1 : 2378
## Un_KI270420v1 : 2321
## Un_KI270509v1 : 2318
## Un_KI270315v1 : 2276
## Un_KI270302v1 : 2274
## Un_KI270518v1 : 2186
## Un_KI270530v1 : 2168
## Un_KI270304v1 : 2165
## Un_KI270418v1 : 2145
## Un_KI270424v1 : 2140
## Un_KI270417v1 : 2043
## Un_KI270508v1 : 1951
## Un_KI270303v1 : 1942
## Un_KI270381v1 : 1930
## Un_KI270529v1 : 1899
## Un_KI270425v1 : 1884
## Un_KI270396v1 : 1880
## Un_KI270363v1 : 1803
## Un_KI270386v1 : 1788
## Un_KI270465v1 : 1774
## Un_KI270383v1 : 1750
## Un_KI270384v1 : 1658
## Un_KI270330v1 : 1652
## Un_KI270372v1 : 1650
## Un_KI270548v1 : 1599
## Un_KI270580v1 : 1553
## Un_KI270387v1 : 1537
## Un_KI270391v1 : 1484
## Un_KI270305v1 : 1472
## Un_KI270373v1 : 1451
## Un_KI270422v1 : 1445
## Un_KI270316v1 : 1444
## Un_KI270338v1 : 1428
## Un_KI270340v1 : 1428
## Un_KI270583v1 : 1400
## Un_KI270334v1 : 1368
## Un_KI270429v1 : 1361
## Un_KI270393v1 : 1308
## Un_KI270516v1 : 1300
## Un_KI270389v1 : 1298
## Un_KI270466v1 : 1233
## Un_KI270388v1 : 1216
## Un_KI270544v1 : 1202
## Un_KI270310v1 : 1201
## Un_KI270412v1 : 1179
## Un_KI270395v1 : 1143
## Un_KI270376v1 : 1136
## Un_KI270337v1 : 1121
## Un_KI270335v1 : 1048
## Un_KI270378v1 : 1048
## Un_KI270379v1 : 1045
## Un_KI270329v1 : 1040
## Un_KI270419v1 : 1029
## Un_KI270336v1 : 1026
## Un_KI270312v1 : 998
## Un_KI270539v1 : 993
## Un_KI270385v1 : 990
## Un_KI270423v1 : 981
## Un_KI270392v1 : 971
## Un_KI270394v1 : 970Once we have an object of the chromLocation class, we can now access its various slots to get the information contained within it. There are six slots in this class:
organism: This lists the organism that this object is describing.
dataSource: Where this data was acquired from.
chromLocs: A list with an element for every unique chromosome
name, where each element contains a named vector where
the names are probe IDs and the values describe the
location of that probe on the chromosome. Negative
values indicate that the location is on the antisense
strand.
probesToChrom: A hash table which will translate a probe ID to the
chromosome it belongs to.
chromInfo: A numerical vector representing each chromosome, where
the names are the names of the chromosomes and the
values are the lengths of those chromosomes.
geneSymbols: An environment that maps a probe ID to the appropriate
gene symbol.There is a basic ‘get’ type method for each of these slots, all with the same
name as the respective slot. In the following example, we will demonstrate these
basic methods. For the probesToChrom and geneSymbols methods, the return
value is an environment which maps a probe ID to other values, we will be using
the probe ID ‘32972_at’, which was selected at random for these examples. We are
showing only part of the chromLocs method’s output as it is quite long in its
entirety.
organism(z)## [1] "Homo sapiens"dataSource(z)## [1] "hgu95av2"## The chromLocs list is extremely large. Let's only
## look at one of the elements.
names(chromLocs(z))## [1] "1" "10" "11"
## [4] "12" "13" "14"
## [7] "15" "16" "17"
## [10] "18" "19" "2"
## [13] "20" "21" "22"
## [16] "22_KI270879v1_alt" "3" "4"
## [19] "5" "6" "7"
## [22] "8" "9" "X"
## [25] "Y" "14_KZ208920v1_fix" "17_KV766198v1_alt"
## [28] "7_KZ208912v1_fix" "17_KI270857v1_alt" "20_KI270869v1_alt"
## [31] "10_KQ090021v1_fix" "17_KV575245v1_fix" "19_KI270867v1_alt"
## [34] "2_KN538363v1_fix" "16_KI270853v1_alt" "15_KI270849v1_alt"
## [37] "1_KQ458383v1_alt" "8_KZ208914v1_fix" "11_KQ759759v1_fix"
## [40] "2_GL383522v1_alt" "13_KI270842v1_alt" "17_GL383564v2_alt"
## [43] "6_GL000251v2_alt" "8_KZ208915v1_fix" "19_KQ458386v1_fix"
## [46] "11_KN196481v1_fix" "11_KI270831v1_alt" "6_GL000254v2_alt"
## [49] "6_GL000256v2_alt" "20_KI270870v1_alt" "19_KI270866v1_alt"
## [52] "8_KI270822v1_alt" "8_KI270819v1_alt" "17_GL383563v3_alt"
## [55] "2_KZ208908v1_alt" "1_GL383519v1_alt" "19_KN196484v1_fix"
## [58] "4_GL000257v2_alt" "2_KI270776v1_alt" "14_KI270846v1_alt"
## [61] "22_KI270875v1_alt" "19_KI270868v1_alt" "8_KI270821v1_alt"
## [64] "16_KZ559113v1_fix" "11_KI270721v1_random" "9_KN196479v1_fix"
## [67] "7_KI270803v1_alt" "15_KI270850v1_alt" "17_JH159146v1_alt"
## [70] "12_KN538369v1_fix" "8_KI270816v1_alt" "14_KI270847v1_alt"
## [73] "16_KQ090026v1_alt" "16_KV880768v1_fix" "11_KI270832v1_alt"
## [76] "17_KI270861v1_alt" "12_KN538370v1_fix" "11_KZ559109v1_fix"
## [79] "3_KN196475v1_fix" "7_KZ208913v1_alt" "22_KQ759762v1_fix"
## [82] "11_KZ559110v1_alt" "1_KZ208904v1_alt" "5_KI270791v1_alt"
## [85] "8_KI270814v1_alt" "18_KQ090028v1_fix" "9_GL383540v1_alt"
## [88] "6_KQ090016v1_fix" "4_GL383527v1_alt" "7_KI270808v1_alt"
## [91] "7_KV880765v1_fix" "5_KV575244v1_fix" "3_KN538364v1_fix"
## [94] "17_KI270862v1_alt" "19_GL383574v1_alt" "22_KI270877v1_alt"
## [97] "12_KZ208916v1_fix" "17_KI270860v1_alt" "1_KI270762v1_alt"
## [100] "4_KQ090015v1_alt" "7_KI270809v1_alt" "10_KI270825v1_alt"
## [103] "1_GL383518v1_alt" "11_KI270830v1_alt" "11_KI270903v1_alt"
## [106] "17_KI270909v1_alt" "8_KI270813v1_alt" "21_KI270873v1_alt"
## [109] "5_KI270795v1_alt" "5_KI270898v1_alt" "7_KI270806v1_alt"
## [112] "6_GL000255v2_alt" "3_KZ559103v1_alt" "12_GL877876v1_alt"
## [115] "12_KI270904v1_alt" "20_KI270871v1_alt" "15_KN538374v1_fix"
## [118] "15_KI270905v1_alt" "17_KI270908v1_alt" "17_GL000258v2_alt"
## [121] "11_KI270927v1_alt" "6_KI270801v1_alt" "5_GL339449v2_alt"
## [124] "10_GL383546v1_alt" "11_KZ559111v1_alt" "13_KN538371v1_fix"
## [127] "19_GL949746v1_alt" "19_GL949752v1_alt" "19_KI270938v1_alt"
## [130] "19_GL949747v2_alt" "19_GL949753v2_alt" "2_KQ983256v1_alt"
## [133] "1_KI270763v1_alt" "22_KI270734v1_random" "12_GL877875v1_alt"
## [136] "15_KQ031389v1_alt" "1_KV880763v1_alt" "1_KQ458384v1_alt"
## [139] "2_GL582966v2_alt" "12_KI270833v1_alt" "6_GL000252v2_alt"
## [142] "1_KN196474v1_fix" "19_KI270865v1_alt" "16_KI270855v1_alt"
## [145] "16_KQ090027v1_alt" "3_KI270782v1_alt" "8_KI270817v1_alt"
## [148] "2_KI270768v1_alt" "11_KI270902v1_alt" "13_KI270838v1_alt"
## [151] "4_KI270896v1_alt" "4_KQ983257v1_fix" "4_KQ983258v1_alt"
## [154] "2_KI270769v1_alt" "15_KI270851v1_alt" "21_GL383581v2_alt"
## [157] "16_KI270854v1_alt" "3_KV766192v1_fix" "6_GL000250v2_alt"
## [160] "19_GL383575v2_alt" "9_KI270823v1_alt" "22_KN196485v1_alt"
## [163] "22_KI270928v1_alt" "22_GL383582v2_alt" "22_KB663609v1_alt"
## [166] "21_KI270872v1_alt" "5_KI270897v1_alt" "22_KI270876v1_alt"
## [169] "1_KN196473v1_fix" "6_GL000253v2_alt" "8_KI270900v1_alt"
## [172] "8_KI270926v1_alt" "8_KI270818v1_alt" "8_KI270812v1_alt"
## [175] "3_KQ031385v1_fix" "2_KI270774v1_alt" "18_KI270863v1_alt"
## [178] "19_GL383573v1_alt" "7_GL383534v2_alt" "6_KZ208911v1_fix"
## [181] "10_KN196480v1_fix" "12_KI270837v1_alt" "6_KI270758v1_alt"
## [184] "15_KI270848v1_alt" "1_GL383520v2_alt" "22_KQ458387v1_alt"
## [187] "22_KN196486v1_alt" "22_KQ759761v1_alt" "22_KQ458388v1_alt"
## [190] "19_GL949748v2_alt" "19_GL949749v2_alt" "19_GL949750v2_alt"
## [193] "19_GL949751v2_alt" "7_KQ031388v1_fix" "5_KV575243v1_alt"
## [196] "19_KV575250v1_alt" "19_KI270922v1_alt" "19_KV575258v1_alt"
## [199] "19_KI270920v1_alt" "19_KI270917v1_alt" "19_KI270923v1_alt"
## [202] "19_KI270929v1_alt" "19_KI270921v1_alt" "17_KI270910v1_alt"
## [205] "3_KI270934v1_alt" "3_KI270895v1_alt" "3_KI270779v1_alt"
## [208] "3_KI270936v1_alt" "3_KI270935v1_alt" "3_KI270924v1_alt"
## [211] "3_KI270937v1_alt" "19_GL000209v2_alt" "19_KI270882v1_alt"
## [214] "19_KI270883v1_alt" "19_KI270884v1_alt" "19_KI270885v1_alt"
## [217] "19_KI270886v1_alt" "19_KI270887v1_alt" "19_KI270888v1_alt"
## [220] "19_KI270889v1_alt" "19_KI270890v1_alt" "19_KI270891v1_alt"
## [223] "19_KI270914v1_alt" "19_KI270915v1_alt" "19_KI270916v1_alt"
## [226] "19_KI270918v1_alt" "19_KI270919v1_alt" "19_KI270930v1_alt"
## [229] "19_KI270931v1_alt" "19_KI270932v1_alt" "19_KI270933v1_alt"
## [232] "19_KV575246v1_alt" "19_KV575247v1_alt" "19_KV575248v1_alt"
## [235] "19_KV575249v1_alt" "19_KV575251v1_alt" "19_KV575252v1_alt"
## [238] "19_KV575253v1_alt" "19_KV575254v1_alt" "19_KV575255v1_alt"
## [241] "19_KV575256v1_alt" "19_KV575257v1_alt" "19_KV575259v1_alt"
## [244] "19_KV575260v1_alt"chromLocs(z)[["Y"]]## 31534_at 31911_at 32864_at 32991_f_at 35885_at 36321_at 40030_at
## 2935380 13703898 -2786854 -6865917 12701230 12662366 7273971
## 41214_at 34172_s_at 34215_at 34753_at 37583_at 37583_at 38182_at
## 2841601 1591603 1591603 57067864 -19703864 -19705414 19567357
## 38182_at 40097_at 40097_at 40435_at 40436_g_at 41108_at 938_at
## 19567357 20575710 20575775 -1386151 -1386151 -304749 57184215
## 31411_at 31411_at 31411_at 34477_at 34477_at 34477_at 1185_at
## 22984262 24618003 -25030900 -13248378 -13323033 -13297508 1336784
## 1185_at 35073_at 35073_at 36553_at 36553_at 36554_at 36554_at
## 1336615 624343 624343 -1403138 -1403138 -1403138 -1403138
## 39168_at 39168_at 41138_at 41138_at 38355_at 38355_at 38355_at
## -2486434 -2486413 2691294 2691294 12905704 12904785 12904857
## 38355_at 38355_at 32930_f_at 32930_f_at 32930_f_at 32930_f_at 32930_f_at
## 12903998 12904867 14524528 14622020 14522615 14523745 14524573
## 32930_f_at 35447_s_at 35447_s_at 35447_s_at 33665_s_at 33665_s_at 33665_s_at
## 14523504 1595454 1615132 1615058 1268813 1268813 1268813
## 33665_s_at
## 1268813get("32972_at", probesToChrom(z))## [1] "X"chromInfo(z)## 1 2 3
## 248956422 242193529 198295559
## 4 5 6
## 190214555 181538259 170805979
## 7 X 8
## 159345973 156040895 145138636
## 9 11 10
## 138394717 135086622 133797422
## 12 13 14
## 133275309 114364328 107043718
## 15 16 17
## 101991189 90338345 83257441
## 18 20 19
## 80373285 64444167 58617616
## Y 22 21
## 57227415 50818468 46709983
## 8_KZ208915v1_fix 15_ML143371v1_fix 15_KI270905v1_alt
## 6367528 5500449 5161414
## 15_KN538374v1_fix 6_GL000256v2_alt 6_GL000254v2_alt
## 4998962 4929269 4827813
## 6_GL000251v2_alt 6_GL000253v2_alt 6_GL000250v2_alt
## 4795265 4677643 4672374
## 6_GL000255v2_alt 6_GL000252v2_alt 17_KI270857v1_alt
## 4606388 4604811 2877074
## 16_KI270853v1_alt 15_KQ031389v1_alt 5_MU273354v1_fix
## 2659700 2365364 2101585
## 16_KV880768v1_fix 16_KI270728v1_random 17_GL000258v2_alt
## 1927115 1872759 1821992
## 5_GL339449v2_alt 1_MU273333v1_fix 14_KI270847v1_alt
## 1612928 1572686 1511111
## 17_KI270908v1_alt 14_KI270846v1_alt 15_MU273374v1_fix
## 1423190 1351393 1154574
## 5_KI270897v1_alt 7_KI270803v1_alt 19_GL949749v2_alt
## 1144418 1111570 1091841
## 19_KI270938v1_alt 19_GL949750v2_alt 19_GL949748v2_alt
## 1066800 1066390 1064304
## 12_KZ208916v1_fix 21_MU273391v1_fix 19_GL949751v2_alt
## 1046838 1020778 1002683
## 19_GL949746v1_alt 19_GL949752v1_alt 8_KI270821v1_alt
## 987716 987100 985506
## 2_MU273342v1_fix 1_KI270763v1_alt 6_KI270801v1_alt
## 955087 911658 870480
## Y_MU273398v1_fix 1_MU273331v1_alt 19_GL949753v2_alt
## 865743 847441 796479
## 19_GL949747v2_alt 14_MU273373v1_fix 14_KZ208920v1_fix
## 729520 722645 690932
## 7_KZ208913v1_alt 5_KV575244v1_fix 8_KI270822v1_alt
## 680662 673059 624492
## X_MU273395v1_alt 7_KZ208912v1_fix 4_GL000257v2_alt
## 619716 589656 586476
## 12_KI270904v1_alt 9_MU273366v1_fix 4_KI270925v1_alt
## 572349 569668 555799
## 1_KV880763v1_alt 12_KN538369v1_fix 17_MU273380v1_fix
## 551020 541038 538541
## 2_MU273338v1_alt 2_KQ983256v1_alt 21_ML143377v1_fix
## 535251 535088 519485
## 1_MU273330v1_alt 5_MU273355v1_fix 2_MU273339v1_alt
## 516764 508332 500581
## 19_ML143376v1_fix 2_MU273343v1_fix 9_MU273365v1_fix
## 493165 489404 482250
## 2_KQ031384v1_fix 16_KZ559113v1_fix 15_KI270852v1_alt
## 481245 480415 478999
## 3_MU273348v1_fix 3_MU273346v1_fix 7_KV880765v1_fix
## 475876 469342 468267
## 1_KQ031383v1_fix 7_MU273358v1_alt 22_ML143378v1_fix
## 467143 464417 461303
## 1_KN538360v1_fix 10_ML143354v1_fix 3_KN196475v1_fix
## 460100 454963 451168
## 15_KI270727v1_random 9_KI270823v1_alt 11_MU273369v1_fix
## 448248 439082 434831
## 2_MU273337v1_alt 15_KI270850v1_alt 8_MU273362v1_fix
## 431782 430880 429744
## 1_KI270759v1_alt 4_KV766193v1_alt 10_KN538367v1_fix
## 425601 420675 420164
## 3_KN538364v1_fix 22_ML143380v1_fix 3_KV766192v1_fix
## 415308 412368 411654
## 13_ML143366v1_fix 12_GL877876v1_alt 18_KQ090028v1_fix
## 409912 408271 407387
## 19_KQ458386v1_fix X_ML143381v1_fix 14_ML143367v1_fix
## 405389 403128 399183
## 15_ML143372v1_fix Un_KI270442v1 17_KI270862v1_alt
## 396515 392061 391357
## 15_GL383555v2_alt 19_GL383573v1_alt 6_MU273357v1_alt
## 388773 385657 383128
## 4_KI270896v1_alt 4_GL383528v1_alt 17_GL383563v3_alt
## 378547 376187 375691
## 8_KI270810v1_alt 3_KQ031385v1_fix 17_MU273378v1_alt
## 374415 373699 372839
## 19_KN196484v1_fix 15_ML143370v1_fix 1_GL383520v2_alt
## 370917 369264 366580
## 2_KN538363v1_fix 5_KV575243v1_alt 13_KN538372v1_fix
## 365499 362221 356766
## 20_MU273389v1_fix 1_KI270762v1_alt 1_KQ458383v1_alt
## 355731 354444 349938
## 11_MU273370v1_fix 4_ML143345v1_fix 9_MU273364v1_fix
## 344606 341066 340717
## 21_MU273390v1_fix 1_MU273332v1_alt 16_MU273377v1_fix
## 336752 335159 334997
## 19_MU273384v1_fix X_MU273397v1_alt 9_KN196479v1_fix
## 333754 330493 330164
## 1_KZ208906v1_fix 15_KI270848v1_alt 17_KI270909v1_alt
## 330031 327382 325800
## 14_KI270844v1_alt 6_KQ031387v1_fix 8_KI270900v1_alt
## 322166 320750 318687
## 12_KQ759760v1_fix 10_GL383546v1_alt 4_MU273349v1_alt
## 315610 309802 308682
## 13_KI270838v1_alt 3_KN196476v1_fix 8_KI270816v1_alt
## 306913 305979 305841
## 1_KN538361v1_fix 11_KZ559108v1_fix 22_KI270879v1_alt
## 305542 305244 304135
## 3_KZ559103v1_alt 5_MU273356v1_alt 11_KZ559110v1_alt
## 302885 302485 301637
## 3_MU273347v1_fix 8_KI270813v1_alt 12_ML143361v1_fix
## 301310 300230 297568
## 11_KI270831v1_alt 15_GL383554v1_alt X_MU273396v1_alt
## 296895 296527 294119
## 19_KV575249v1_alt 10_ML143355v1_fix 8_KI270811v1_alt
## 293522 292944 292436
## 18_GL383567v1_alt 2_MU273340v1_alt X_KI270880v1_alt
## 289831 284971 284869
## 8_KI270812v1_alt 19_KI270921v1_alt 17_KV766196v1_fix
## 282736 282224 281919
## 17_KI270729v1_random 11_KZ559109v1_fix 1_KQ983255v1_alt
## 280839 279644 278659
## 17_JH159146v1_alt 10_KN196480v1_fix 17_KV766198v1_alt
## 278131 277797 276292
## 4_ML143349v1_fix X_KI270913v1_alt 20_MU273388v1_fix
## 276109 274009 273725
## 6_KI270798v1_alt 7_KI270808v1_alt 16_ML143373v1_fix
## 271782 271455 270967
## 11_ML143358v1_fix 6_KN196478v1_fix 16_KQ090027v1_alt
## 270122 268330 267463
## 8_KV880767v1_fix 10_KQ090021v1_fix 14_ML143368v1_alt
## 265876 264545 264228
## 22_KI270876v1_alt 15_KI270851v1_alt 11_MU273368v1_alt
## 263666 263054 261194
## 22_KI270875v1_alt 1_KI270766v1_alt 7_ML143352v1_fix
## 259914 256271 254759
## 1_MU273336v1_fix 19_KI270882v1_alt 3_KI270778v1_alt
## 250447 248807 248252
## 17_KV766197v1_alt 6_KQ090016v1_fix 15_KI270849v1_alt
## 246895 245716 244917
## 2_MU273344v1_fix 4_KI270786v1_alt 6_KZ208911v1_fix
## 244725 244096 242796
## 19_KV575250v1_alt 12_KI270835v1_alt 4_KQ090015v1_alt
## 241058 238139 236512
## 17_KI270858v1_alt 4_ML143344v1_fix 17_MU273379v1_fix
## 235827 235734 234878
## 19_KI270867v1_alt 16_KI270855v1_alt 18_KZ559115v1_fix
## 233762 232857 230843
## 4_KQ983257v1_fix 8_KI270926v1_alt 5_GL949742v1_alt
## 230434 229282 226852
## 19_MU273386v1_fix 3_KI270780v1_alt 17_GL383565v1_alt
## 226166 224108 223995
## 2_KI270774v1_alt 19_KV575256v1_alt 4_KI270790v1_alt
## 223625 223118 220246
## 11_KI270927v1_alt 11_ML143359v1_fix 19_KI270932v1_alt
## 218612 217075 215732
## 3_ML143343v1_alt 11_KI270903v1_alt 2_KI270894v1_alt
## 215443 214625 214158
## 1_KQ458384v1_alt 1_MU273335v1_fix 12_KN196482v1_fix
## 212205 211934 211377
## 14_GL000225v1_random Un_KI270743v1 1_MU273334v1_fix
## 211173 210658 210426
## 11_KI270832v1_alt 7_KI270805v1_alt Y_KZ208924v1_fix
## 210133 209988 209722
## 4_GL000008v2_random 7_KI270809v1_alt 19_KI270887v1_alt
## 209709 209586 209512
## 5_MU273353v1_fix 2_KN538362v1_fix 8_MU273363v1_fix
## 208405 208149 207371
## 13_KN538371v1_fix 4_KI270789v1_alt 4_MU273351v1_fix
## 206320 205944 205691
## 4_KQ983258v1_alt 3_KI270779v1_alt 19_KI270914v1_alt
## 205407 205312 205194
## 18_KQ458385v1_alt 11_KQ759759v2_fix 19_KI270886v1_alt
## 205101 204999 204239
## 11_KI270829v1_alt 15_MU273375v1_alt 11_KN538368v1_alt
## 204059 204007 203552
## 14_GL000009v2_random 21_GL383579v2_alt 11_JH159136v1_alt
## 201709 201197 200998
## 19_KI270930v1_alt Un_KI270747v1 18_GL383571v1_alt
## 200773 198735 198278
## 19_KI270920v1_alt 3_KZ559102v1_alt 6_KI270797v1_alt
## 198005 197752 197536
## 3_KI270935v1_alt 11_KQ759759v1_fix 17_KI270861v1_alt
## 197351 196940 196688
## 15_KI270906v1_alt 10_MU273367v1_fix 5_KI270791v1_alt
## 196384 196262 195710
## 3_KZ559105v1_alt 14_KI270722v1_random 12_ML143362v1_fix
## 195063 194050 192531
## 16_GL383556v1_alt 13_KI270840v1_alt 14_GL000194v1_random
## 192462 191684 191469
## 11_JH159137v1_alt 19_KI270917v1_alt 7_KI270899v1_alt
## 191409 190932 190869
## 21_MU273392v1_fix 19_KI270923v1_alt 10_KI270825v1_alt
## 189707 189352 188315
## 19_GL383576v1_alt X_KV766199v1_alt 19_KI270922v1_alt
## 188024 188004 187935
## 17_MU273382v1_fix Un_KI270742v1 1_KN196472v1_fix
## 187626 186739 186494
## 22_KI270878v1_alt 19_KI270929v1_alt 11_KI270826v1_alt
## 186262 186203 186169
## 6_KB021644v2_alt 17_GL000205v2_random 10_KQ090020v1_alt
## 185823 185591 185507
## 1_KI270765v1_alt 19_KI270916v1_alt 19_KI270890v1_alt
## 185285 184516 184499
## 3_KI270784v1_alt 12_GL383551v1_alt 20_KI270870v1_alt
## 184404 184319 183433
## Un_GL000195v1 1_GL383518v1_alt 11_KQ090022v1_fix
## 182896 182439 181958
## 22_KI270736v1_random 2_KZ208907v1_alt 10_KI270824v1_alt
## 181920 181658 181496
## 11_KZ559111v1_alt 14_KI270845v1_alt 3_GL383526v1_alt
## 181167 180703 180671
## 13_KI270839v1_alt 7_KQ031388v1_fix 22_KI270733v1_random
## 180306 179932 179772
## Un_GL000224v1 10_GL383545v1_alt Un_GL000219v1
## 179693 179254 179198
## 5_KI270792v1_alt 17_KI270860v1_alt 19_KV575252v1_alt
## 179043 178921 178197
## 19_GL000209v2_alt 11_KI270830v1_alt 9_KI270719v1_random
## 177381 177092 176845
## 4_ML143347v1_fix Un_GL000216v2 22_KI270928v1_alt
## 176674 176608 176103
## 1_KI270712v1_random 3_KZ208909v1_alt 6_KI270800v1_alt
## 176043 175849 175808
## 1_KI270706v1_random 12_KZ208918v1_alt 22_KQ458388v1_alt
## 175055 174808 174749
## 2_MU273345v1_fix 2_KI270776v1_alt 18_KI270912v1_alt
## 174385 174166 174061
## 3_KI270777v1_alt 5_GL383531v1_alt 3_JH636055v2_alt
## 173649 173459 173151
## 14_KI270725v1_random 5_KI270796v1_alt 17_MU273383v1_fix
## 172810 172708 172609
## 7_KZ559106v1_alt 14_KZ208919v1_alt 9_GL383541v1_alt
## 172555 171798 171286
## 19_KV575259v1_alt 19_KI270885v1_alt 11_ML143360v1_fix
## 171263 171027 170928
## 19_KI270919v1_alt 19_KI270889v1_alt 19_KI270891v1_alt
## 170701 170698 170680
## 19_KI270915v1_alt 19_KI270933v1_alt 19_KI270883v1_alt
## 170665 170537 170399
## 19_GL383575v2_alt 19_KV575247v1_alt 19_KI270931v1_alt
## 170222 170206 170148
## 12_GL383550v2_alt 16_KQ031390v1_alt 13_KI270841v1_alt
## 169178 169136 169134
## Un_KI270744v1 13_KQ090024v1_alt 19_KV575248v1_alt
## 168472 168146 168131
## 18_KI270863v1_alt 18_GL383569v1_alt 12_GL877875v1_alt
## 167999 167950 167313
## 21_KI270874v1_alt 19_KV575253v1_alt 3_KI270924v1_alt
## 166743 166713 166540
## 1_KN196473v1_fix 1_KZ208904v1_alt 1_KI270761v1_alt
## 166200 166136 165834
## 3_KQ031386v1_fix 3_KI270937v1_alt 11_ML143357v1_fix
## 165718 165607 165419
## 8_KZ208914v1_fix 22_KI270734v1_random 18_GL383570v1_alt
## 165120 165050 164789
## 5_KI270794v1_alt 4_GL383527v1_alt Un_GL000213v1
## 164558 164536 164239
## 3_KI270936v1_alt 3_KZ559101v1_alt 19_KV575246v1_alt
## 164170 164041 163926
## 9_KQ090018v1_alt 4_KQ090014v1_alt 3_KI270934v1_alt
## 163882 163749 163458
## 18_KZ559116v1_alt 9_GL383539v1_alt 3_KI270895v1_alt
## 163186 162988 162896
## 22_GL383582v2_alt 3_KI270782v1_alt 1_KI270892v1_alt
## 162811 162429 162212
## Un_GL000220v1 2_KI270767v1_alt 2_KI270715v1_random
## 161802 161578 161471
## 2_KI270893v1_alt Un_GL000218v1 19_KV575255v1_alt
## 161218 161147 161095
## 18_GL383572v1_alt 19_KV575251v1_alt 8_KI270817v1_alt
## 159547 159285 158983
## 4_KI270788v1_alt 13_ML143364v1_fix Un_KI270749v1
## 158965 158944 158759
## 7_KI270806v1_alt 7_KI270804v1_alt 18_KI270911v1_alt
## 158166 157952 157710
## Un_KI270741v1 17_KI270910v1_alt 19_KI270884v1_alt
## 157432 157099 157053
## 8_KV880766v1_fix 19_KV575258v1_alt 22_KN196485v1_alt
## 156998 156965 156562
## 22_KQ458387v1_alt 19_GL383574v1_alt 19_KI270888v1_alt
## 155930 155864 155532
## 3_GL000221v1_random 17_KV575245v1_fix 11_GL383547v1_alt
## 155397 154723 154407
## 12_KZ559112v1_alt 2_KI270716v1_random 22_KN196486v1_alt
## 154139 153799 153027
## 12_GL383553v2_alt 6_KI270799v1_alt 22_KI270731v1_random
## 152874 152148 150754
## Un_KI270751v1 8_MU273359v1_fix Un_KI270750v1
## 150742 150302 148850
## 13_KN538373v1_fix 2_ML143341v1_fix 19_KV575260v1_alt
## 148762 145975 145691
## 8_KI270818v1_alt 22_KQ759761v1_alt 17_MU273381v1_fix
## 145606 145162 144689
## X_KI270881v1_alt 21_KI270873v1_alt 2_GL383521v1_alt
## 144206 143900 143390
## 7_KV880764v1_fix 8_KI270814v1_alt 1_KQ458382v1_alt
## 142129 141812 141019
## 11_KV766195v1_fix X_MU273394v1_fix 2_KZ208908v1_alt
## 140877 140567 140361
## 1_KZ208905v1_alt 6_KV766194v1_fix 5_KN196477v1_alt
## 140355 139427 139087
## 12_GL383552v1_alt Un_KI270519v1 2_KI270775v1_alt
## 138655 138126 138019
## 17_ML143374v1_fix 19_MU273385v1_fix 17_KI270907v1_alt
## 137908 137818 137721
## Un_GL000214v1 8_KI270901v1_alt 2_KI270770v1_alt
## 137718 136959 136240
## 5_KZ208910v1_alt 16_KI270854v1_alt 9_KQ090019v1_alt
## 135987 134193 134099
## 8_KI270819v1_alt 17_GL383564v2_alt 2_KI270772v1_alt
## 133535 133151 133041
## 8_KI270815v1_alt 5_KI270795v1_alt 5_KI270898v1_alt
## 132244 131892 130957
## 20_GL383577v2_alt 1_KI270708v1_random 7_KI270807v1_alt
## 128386 127682 126434
## 5_KI270793v1_alt 4_ML143348v1_fix 6_GL383533v1_alt
## 126136 125549 124736
## 2_GL383522v1_alt 13_KQ090025v1_alt 19_KI270918v1_alt
## 123821 123480 123111
## 11_MU273371v1_fix 1_KN196474v1_fix 12_GL383549v1_alt
## 122722 122022 120804
## 2_KI270769v1_alt 2_MU273341v1_fix 4_KI270785v1_alt
## 120616 120381 119912
## 12_KI270834v1_alt 7_GL383534v2_alt 20_KI270869v1_alt
## 119498 119183 118774
## 17_KZ559114v1_alt 21_GL383581v2_alt 4_MU273350v1_fix
## 116753 116689 113364
## 3_KI270781v1_alt 17_KI270730v1_random Un_KI270438v1
## 113034 112551 112505
## 4_KI270787v1_alt 18_KI270864v1_alt 2_KI270771v1_alt
## 111943 111737 110395
## 1_GL383519v1_alt 2_KI270768v1_alt 1_KI270760v1_alt
## 110268 110099 109528
## 12_KQ090023v1_alt 3_KI270783v1_alt 11_KN196481v1_fix
## 109323 109187 108875
## 17_KI270859v1_alt 8_MU273361v1_fix 11_KI270902v1_alt
## 108763 106905 106711
## 3_KZ559104v1_fix 18_GL383568v1_alt 12_MU273372v1_fix
## 105527 104552 104537
## 22_KI270737v1_random 13_KI270843v1_alt 8_KZ559107v1_alt
## 103838 103832 103072
## 22_KI270877v1_alt 5_GL383530v1_alt Y_KN196487v1_fix
## 101331 101241 101150
## 22_KQ759762v2_fix 22_KQ759762v1_fix 19_KV575257v1_alt
## 101040 101037 100553
## 11_KI270721v1_random 19_KV575254v1_alt 22_KI270738v1_random
## 100316 99845 99375
## 15_ML143369v1_fix 22_GL383583v2_alt 2_GL582966v2_alt
## 97763 96924 96131
## Un_KI270748v1 18_KZ208922v1_fix Un_KI270435v1
## 93321 93070 92983
## 5_GL000208v1_random Un_KI270538v1 4_KQ090013v1_alt
## 92689 91309 90922
## 17_GL383566v1_alt 5_ML143350v1_fix 16_GL383557v1_alt
## 90219 89956 89672
## 19_MU273387v1_alt 17_JH159148v1_alt 16_MU273376v1_fix
## 89211 88070 87715
## 12_KN538370v1_fix 10_KN538366v1_fix 2_ML143342v1_fix
## 86533 85284 84043
## 5_GL383532v1_alt 21_KI270872v1_alt 6_KQ090017v1_alt
## 82728 82692 82315
## Un_KI270756v1 16_KZ208921v1_alt 6_KI270758v1_alt
## 79590 78609 76752
## 12_KI270833v1_alt 6_KI270802v1_alt 21_GL383580v2_alt
## 76061 75005 74653
## 22_KB663609v1_alt 22_KI270739v1_random 6_ML143351v1_fix
## 74013 73985 73265
## 9_GL383540v1_alt Un_KI270757v1 2_KI270773v1_alt
## 71551 71251 70887
## 17_JH159147v1_alt X_MU273393v1_fix X_ML143383v1_fix
## 70345 68810 68192
## 11_KI270827v1_alt 1_KI270709v1_random Un_KI270746v1
## 67707 66860 66486
## 13_ML143365v1_fix 12_KZ208917v1_fix 16_KI270856v1_alt
## 65394 64689 63982
## 21_GL383578v2_alt Un_KI270753v1 19_KI270868v1_alt
## 63917 62944 61734
## 9_GL383542v1_alt 16_KQ090026v1_alt 20_KI270871v1_alt
## 60032 59016 58661
## 17_ML143375v1_fix 12_KI270836v1_alt 4_ML143346v1_fix
## 56695 56134 53476
## 19_KI270865v1_alt 1_KI270764v1_alt Y_KZ208923v1_fix
## 52969 50258 48370
## 11_ML143356v1_fix 1_KZ559100v1_fix Un_KI270589v1
## 45257 44955 44474
## 14_KI270726v1_random 19_KI270866v1_alt 22_KI270735v1_random
## 43739 43156 42811
## 1_KI270711v1_random Un_KI270745v1 1_KI270714v1_random
## 42210 41891 41717
## 22_KI270732v1_random 1_KI270713v1_random Un_KI270754v1
## 41543 40745 40191
## 1_KI270710v1_random 12_KI270837v1_alt 9_KI270717v1_random
## 40176 40090 40062
## 14_KI270724v1_random 8_MU273360v1_fix 9_KI270720v1_random
## 39555 39290 39050
## 14_KI270723v1_random 9_KI270718v1_random Un_KI270317v1
## 38115 38054 37690
## 13_KI270842v1_alt Y_KI270740v1_random Un_KI270755v1
## 37287 37240 36723
## 8_KI270820v1_alt 13_KN196483v1_fix 5_MU273352v1_fix
## 36640 35455 34400
## 1_KI270707v1_random Un_KI270579v1 X_ML143382v1_fix
## 32032 31033 28824
## Un_KI270752v1 9_ML143353v1_fix Un_KI270512v1
## 27745 25408 22689
## Un_KI270322v1 X_ML143385v1_fix M
## 21476 17435 16569
## Un_GL000226v1 X_ML143384v1_fix 10_KN538365v1_fix
## 15008 14678 14347
## Un_KI270311v1 22_ML143379v1_fix Un_KI270366v1
## 12399 12295 8320
## Un_KI270511v1 Un_KI270448v1 Un_KI270521v1
## 8127 7992 7642
## 13_ML143363v1_fix Un_KI270581v1 Un_KI270582v1
## 7309 7046 6504
## Un_KI270515v1 Un_KI270588v1 Un_KI270591v1
## 6361 6158 5796
## Un_KI270522v1 Un_KI270507v1 Un_KI270590v1
## 5674 5353 4685
## Un_KI270584v1 Un_KI270320v1 Un_KI270382v1
## 4513 4416 4215
## Un_KI270468v1 Un_KI270467v1 Un_KI270362v1
## 4055 3920 3530
## Un_KI270517v1 Un_KI270593v1 Un_KI270528v1
## 3253 3041 2983
## Un_KI270587v1 Un_KI270364v1 Un_KI270371v1
## 2969 2855 2805
## Un_KI270333v1 Un_KI270374v1 Un_KI270411v1
## 2699 2656 2646
## Un_KI270414v1 Un_KI270510v1 Un_KI270390v1
## 2489 2415 2387
## Un_KI270375v1 Un_KI270420v1 Un_KI270509v1
## 2378 2321 2318
## Un_KI270315v1 Un_KI270302v1 Un_KI270518v1
## 2276 2274 2186
## Un_KI270530v1 Un_KI270304v1 Un_KI270418v1
## 2168 2165 2145
## Un_KI270424v1 Un_KI270417v1 Un_KI270508v1
## 2140 2043 1951
## Un_KI270303v1 Un_KI270381v1 Un_KI270529v1
## 1942 1930 1899
## Un_KI270425v1 Un_KI270396v1 Un_KI270363v1
## 1884 1880 1803
## Un_KI270386v1 Un_KI270465v1 Un_KI270383v1
## 1788 1774 1750
## Un_KI270384v1 Un_KI270330v1 Un_KI270372v1
## 1658 1652 1650
## Un_KI270548v1 Un_KI270580v1 Un_KI270387v1
## 1599 1553 1537
## Un_KI270391v1 Un_KI270305v1 Un_KI270373v1
## 1484 1472 1451
## Un_KI270422v1 Un_KI270316v1 Un_KI270338v1
## 1445 1444 1428
## Un_KI270340v1 Un_KI270583v1 Un_KI270334v1
## 1428 1400 1368
## Un_KI270429v1 Un_KI270393v1 Un_KI270516v1
## 1361 1308 1300
## Un_KI270389v1 Un_KI270466v1 Un_KI270388v1
## 1298 1233 1216
## Un_KI270544v1 Un_KI270310v1 Un_KI270412v1
## 1202 1201 1179
## Un_KI270395v1 Un_KI270376v1 Un_KI270337v1
## 1143 1136 1121
## Un_KI270335v1 Un_KI270378v1 Un_KI270379v1
## 1048 1048 1045
## Un_KI270329v1 Un_KI270419v1 Un_KI270336v1
## 1040 1029 1026
## Un_KI270312v1 Un_KI270539v1 Un_KI270385v1
## 998 993 990
## Un_KI270423v1 Un_KI270392v1 Un_KI270394v1
## 981 971 970get("32972_at", geneSymbols(z))## [1] "NOX1"Another method which can be used to access information about the particular
chromLocation object is the nChrom method, which will list how many
chromosomes this organism has:
nChrom(z)## [1] 711The chromLocation class has a simple design, but can be powerful if one wants to store the chromosomal data contained in a Bioconductor package into a single object. These objects can be created once and then passed around to multiple functions, which can cut down on computation time to access the desired information from the package. These objects allow access to basic but also important information, and provide a standard interface for writers of other software to access this information.