Extract the directional effect-allele (A1) frequency vector for
a QtlDataset. Unlike getMaf, the value is not
folded to the minor allele: it is the frequency of the dosage-counted
allele (A1, the effect allele), matching the allele the marginal effect
sizes and the fine-mapping af column report.
Usage
getAf(x, ...)
# S4 method for class 'QtlDataset'
getAf(x, traitId = NULL, region = NULL, cisWindow = NULL, samples = NULL, ...)Arguments
- x
A
QtlDatasetobject.- ...
Class-specific selection arguments (e.g.,
traitId,region,cisWindow,samplesforQtlDataset).- traitId
Character or
NULL. Molecular trait / feature identifier to select;NULLmatches all traits in the dataset.- region
Character (length 1,
"chr:start-end") orNULL. Restrict variants to this region;NULLuses the full cis window / all regions.- cisWindow
Integer or
NULL. Half-width (bp) of the cis window around the trait;NULLuses the dataset default.- samples
Character vector or
NULL. Restrict to these sample IDs;NULLuses all samples.
Value
Named numeric vector of effect-allele frequencies (names are variant IDs), or an empty vector when no variants are selected.
Examples
data(qtlDatasetExample)
getAf(qtlDatasetExample)
#> chr22:14560203:A:G chr22:14564328:T:C chr22:14850625:T:G chr22:14870204:T:C
#> 0.07575758 0.17575758 0.12727273 0.35151515
#> chr22:14878387:G:A chr22:14880040:A:G chr22:14884399:T:C chr22:15063831:A:G
#> 0.16564417 0.17878788 0.13636364 0.11212121
#> chr22:15257135:C:G chr22:15266873:A:G chr22:15268900:C:G chr22:15298335:T:C
#> 0.07098765 0.27187500 0.29629630 0.34782609
#> chr22:15380277:C:T chr22:15412698:T:C chr22:15434720:T:C chr22:15435569:G:T
#> 0.41049383 0.44207317 0.25454545 0.47515528
#> chr22:15437138:T:G chr22:15438616:C:T chr22:15445079:T:A chr22:15447005:T:C
#> 0.05151515 0.13043478 0.25460123 0.02727273
#> chr22:15447504:T:G chr22:15452483:G:A chr22:15454622:C:A chr22:15455353:A:C
#> 0.29393939 0.09393939 0.09393939 0.20000000
#> chr22:15460378:G:A chr22:15464609:G:A chr22:15467656:A:C chr22:15474749:C:A
#> 0.14506173 0.35454545 0.35365854 0.14848485
#> chr22:15476864:T:C chr22:15480497:C:T chr22:15483717:T:G chr22:15492342:C:T
#> 0.26363636 0.12962963 0.26363636 0.06172840
#> chr22:15496398:T:G chr22:15498747:C:T chr22:15509738:T:C chr22:15512490:A:G
#> 0.14814815 0.26851852 0.31055901 0.14417178
#> chr22:15529033:G:C chr22:15532611:A:G chr22:15534984:A:G chr22:15535383:A:G
#> 0.31595092 0.32727273 0.05757576 0.13803681
#> chr22:15544773:T:C chr22:15549522:A:G chr22:15551377:C:T chr22:15557470:C:T
#> 0.33636364 0.28787879 0.31402439 0.01212121
#> chr22:15558213:G:A chr22:15558230:C:T chr22:15558586:G:A chr22:15558924:A:T
#> 0.49696970 0.03939394 0.31818182 0.41614907
#> chr22:15563103:C:T chr22:15567276:C:T chr22:15567719:G:A chr22:15569194:A:G
#> 0.06363636 0.19938650 0.30368098 0.20061728
#> chr22:15570730:C:T chr22:15576300:C:T chr22:15583103:G:A chr22:15591075:A:G
#> 0.20000000 0.11818182 0.26397516 0.36956522
#> chr22:15594252:T:C chr22:15594669:T:C chr22:15601495:T:C chr22:15603938:T:C
#> 0.17378049 0.17878788 0.33636364 0.49695122
#> chr22:15607461:C:T chr22:15611133:C:G chr22:15611603:T:C chr22:15618270:G:C
#> 0.19393939 0.16257669 0.11818182 0.05214724
#> chr22:15618335:C:A chr22:15619552:T:C chr22:15625340:G:A chr22:15626329:C:T
#> 0.40797546 0.13190184 0.11515152 0.30674847
#> chr22:15634399:C:T chr22:15636231:C:A chr22:15637198:C:T chr22:15638201:T:C
#> 0.30745342 0.26666667 0.41562500 0.31481481
#> chr22:15639954:G:A chr22:15641026:G:A chr22:15643854:G:C chr22:15644565:T:G
#> 0.13939394 0.32424242 0.11963190 0.11515152
#> chr22:15644904:A:G chr22:15645124:C:A chr22:15645194:G:A chr22:15647006:T:C
#> 0.41818182 0.11515152 0.36969697 0.11212121
#> chr22:15648016:C:T chr22:15649076:T:C chr22:15651652:C:T chr22:15651703:C:T
#> 0.11656442 0.11818182 0.11963190 0.11515152
#> chr22:15653728:T:C chr22:15654435:T:C chr22:15655394:G:A chr22:15658762:T:C
#> 0.35365854 0.13496933 0.30182927 0.05151515
#> chr22:15660822:G:A chr22:15661931:G:A chr22:15664065:T:C chr22:15665049:C:G
#> 0.05151515 0.30312500 0.29393939 0.14110429
#> chr22:15665949:T:C chr22:15666329:T:G chr22:15666712:T:A chr22:15668988:T:C
#> 0.33333333 0.24242424 0.30368098 0.05454545
#> chr22:15669118:T:C chr22:15674251:T:G chr22:15679901:G:T chr22:15680320:G:A
#> 0.13939394 0.42987805 0.46666667 0.13636364
#> chr22:15681217:A:G chr22:15681843:G:A chr22:15683383:T:C chr22:15683469:T:C
#> 0.46666667 0.15757576 0.42378049 0.42378049
#> chr22:15683596:T:G chr22:15684132:A:G chr22:15684246:T:C chr22:15684887:G:A
#> 0.10909091 0.42424242 0.42424242 0.46666667
#> chr22:15685777:A:G chr22:15686104:T:G chr22:15686270:G:A chr22:15688241:G:A
#> 0.26363636 0.10606061 0.47272727 0.14545455
#> chr22:15689296:A:G chr22:15689362:T:G chr22:15689881:A:G chr22:15690488:C:T
#> 0.10606061 0.38787879 0.24242424 0.38787879
#> chr22:15690741:G:A chr22:15692596:C:T chr22:15693798:C:G chr22:15695102:T:C
#> 0.38787879 0.48787879 0.27878788 0.21212121
#> chr22:15695458:G:T chr22:15695503:A:G chr22:15696313:T:C chr22:15697233:C:A
#> 0.27272727 0.27878788 0.21212121 0.27607362
#> chr22:15697346:T:C chr22:15698150:C:T chr22:15698333:A:G chr22:15698682:T:C
#> 0.49090909 0.46060606 0.02121212 0.46060606
#> chr22:15699156:C:T chr22:15701768:G:C chr22:15704504:G:T chr22:15706181:A:C
#> 0.23170732 0.09815951 0.46060606 0.44848485
#> chr22:15706432:C:T chr22:15706668:G:A chr22:15707595:T:C chr22:15708627:C:T
#> 0.21212121 0.23636364 0.23030303 0.23636364
#> chr22:15709601:T:G chr22:15711656:C:T chr22:15719003:A:G chr22:15719068:C:T
#> 0.01212121 0.01226994 0.24085366 0.23333333
#> chr22:15719404:A:G chr22:15720906:C:T chr22:15732097:G:A chr22:15733947:G:A
#> 0.45151515 0.23475610 0.32926829 0.10303030
#> chr22:15767757:A:G chr22:15771088:G:A chr22:15773876:C:T chr22:15774989:T:C
#> 0.26829268 0.31818182 0.03353659 0.35802469
#> chr22:15775610:G:A chr22:15776459:C:T chr22:15776612:C:T chr22:15777875:T:C
#> 0.26060606 0.05454545 0.24242424 0.23939394
#> chr22:15778508:T:C chr22:15778800:C:T chr22:15778812:A:G chr22:15779211:A:C
#> 0.41515152 0.19393939 0.17575758 0.14634146
#> chr22:15783936:G:C chr22:15784605:A:G chr22:15785173:C:T chr22:15787349:C:T
#> 0.32424242 0.35670732 0.16352201 0.38181818
#> chr22:15787566:C:T chr22:15787755:T:C chr22:15789897:G:A chr22:15789957:G:C
#> 0.16969697 0.26363636 0.12121212 0.26363636
#> chr22:15790373:A:G chr22:15790790:G:A chr22:15791899:A:G chr22:15792216:A:G
#> 0.38181818 0.30303030 0.28484848 0.43597561
#> chr22:15792806:T:C chr22:15794103:T:C chr22:15794640:G:A chr22:15795490:G:A
#> 0.25914634 0.08841463 0.30000000 0.08787879
#> chr22:15795572:T:C chr22:15801989:T:C chr22:15803930:T:C chr22:15806401:T:C
#> 0.07878788 0.32121212 0.08787879 0.31481481
#> chr22:15807037:G:A chr22:15807664:A:C chr22:15808080:T:C chr22:15808123:C:G
#> 0.08787879 0.29090909 0.30303030 0.06363636
#> chr22:15808815:A:G chr22:15808982:A:G chr22:15809384:T:C chr22:15813210:T:G
#> 0.31097561 0.32012195 0.19393939 0.37195122
#> chr22:15814084:G:A chr22:15814521:T:C chr22:15816846:G:A chr22:15817310:C:T
#> 0.32424242 0.09696970 0.46060606 0.34242424
#> chr22:15821524:A:G chr22:15822154:T:C chr22:15822206:A:C chr22:15822223:T:C
#> 0.16060606 0.11818182 0.10606061 0.11818182
#> chr22:15822739:T:C chr22:15822987:C:T chr22:15823131:T:C chr22:15823238:A:T
#> 0.34545455 0.10606061 0.10606061 0.42121212
#> chr22:15823381:G:A chr22:15825502:C:A chr22:15826914:T:G chr22:15826991:T:C
#> 0.33939394 0.45454545 0.10606061 0.31515152