Credible set of genetic variants

Credible set of putative causal variants

credset(pp, CV, thr)

Arguments

pp	Vector of posterior probabilities of causality
CV	Optional parameter: Index of CV
thr	Minimum threshold for credible set size

Value

list of the variants in the credible set, the claimed.cov (cumulative sum of the posterior probabilities of the variants forming the credible set), binary covered indicator (1 if CV is contained in the credible set) and nvar (number of variants in the set)

Details

If the CV parameter is supplied (index of causal variant) then the output includes a binary indicator of whether the CV is contained in the set

Examples

set.seed(1)
nsnps <- 100
pp <- rnorm(nsnps, 0.3, 0.05)
pp <- pp/sum(pp)

credset(pp, thr = 0.9)
#> $credset
#>  [1]  61  70  56   4  95  11  68  55  31  92  83  93  15  39  87  18  21  50  19
#> [20]  22  48  40   8  94  43  63  25  73  85  20   9  59  96  44   7  71  30  51
#> [39]  12  33  89  47  53  86   5  76  90  66   2  69  23  79  64  78  17  62  16
#> [58]  34  26  38  32  49  60  82  27  41  42  88  10  57  37  36  77 100  29  91
#> [77]  81  98  80  52  13   1  45  46  72  65   6
#> 
#> $claimed.cov
#> [1] 0.9019109
#> 
#> $nvar
#> [1] 87
#> 

iCV <- 71

credset(pp, CV = iCV, thr = 0.9)
#> $credset
#>  [1]  61  70  56   4  95  11  68  55  31  92  83  93  15  39  87  18  21  50  19
#> [20]  22  48  40   8  94  43  63  25  73  85  20   9  59  96  44   7  71  30  51
#> [39]  12  33  89  47  53  86   5  76  90  66   2  69  23  79  64  78  17  62  16
#> [58]  34  26  38  32  49  60  82  27  41  42  88  10  57  37  36  77 100  29  91
#> [77]  81  98  80  52  13   1  45  46  72  65   6
#> 
#> $claimed.cov
#> [1] 0.9019109
#> 
#> $covered
#> [1] 1
#> 
#> $nvar
#> [1] 87
#>