Extracts coefficients from an existing mvSuSiE fit or fits `fitMvsusie()` from `X` and `Y`.
Usage
mvsusieWeights(
mvsusieFit = NULL,
X = NULL,
Y = NULL,
priorVariance = NULL,
residualVariance = NULL,
L = 30,
LGreedy = 5,
verbose = FALSE,
...
)Arguments
- mvsusieFit
Optional fitted mvSuSiE object.
- X
Genotype matrix. Required when `mvsusieFit` is NULL.
- Y
Phenotype matrix. Required when `mvsusieFit` is NULL.
- priorVariance
Optional mvSuSiE prior variance list.
- residualVariance
Optional residual variance matrix.
- L
Maximum number of components.
- LGreedy
Initial greedy number of components.
- verbose
If TRUE, prints mvSuSiE fitting progress.
- ...
Additional arguments passed to `fitMvsusie()` when fitting.
Examples
# \donttest{
# Requires susieR attached (mvsusieR 0.3.0 packaging limitation).
library(susieR)
data(multiTraitData)
X <- multiTraitData$X[, 1:60]
Y <- multiTraitData$Y
mvsusieWeights(X = X, Y = Y, L = 5, LGreedy = 2)
#> mvsusieFit is not provided; fitting mvSuSiE now ...
#> cond_1 cond_2 cond_3 cond_4 cond_5
#> chr8:27119632_TA_T 0 0 0 0 0
#> chr8:27119646_A_AG 0 0 0 0 0
#> chr8:27119646_A_G 0 0 0 0 0
#> chr8:27119788_C_T 0 0 0 0 0
#> chr8:27119867_G_T 0 0 0 0 0
#> chr8:27119961_G_T 0 0 0 0 0
#> chr8:27120636_C_T 0 0 0 0 0
#> chr8:27120932_A_G 0 0 0 0 0
#> chr8:27121290_T_C 0 0 0 0 0
#> chr8:27121498_C_A 0 0 0 0 0
#> chr8:27121702_G_A 0 0 0 0 0
#> chr8:27121936_A_G 0 0 0 0 0
#> chr8:27122117_CAA_C 0 0 0 0 0
#> chr8:27122117_CAAA_C 0 0 0 0 0
#> chr8:27122139_A_C 0 0 0 0 0
#> chr8:27122351_G_A 0 0 0 0 0
#> chr8:27123070_G_C 0 0 0 0 0
#> chr8:27123164_C_T 0 0 0 0 0
#> chr8:27123274_T_TG 0 0 0 0 0
#> chr8:27123283_T_TTTTTGTTTTGTTTTG 0 0 0 0 0
#> chr8:27123283_T_TTTTTGTTTTG 0 0 0 0 0
#> chr8:27123283_T_TTTTTGTTTTGTTTTGTTTTG 0 0 0 0 0
#> chr8:27123383_C_T 0 0 0 0 0
#> chr8:27123630_G_C 0 0 0 0 0
#> chr8:27123806_T_C 0 0 0 0 0
#> chr8:27124049_A_G 0 0 0 0 0
#> chr8:27124126_T_C 0 0 0 0 0
#> chr8:27124147_C_A 0 0 0 0 0
#> chr8:27124381_A_G 0 0 0 0 0
#> chr8:27124644_G_A 0 0 0 0 0
#> chr8:27124683_C_T 0 0 0 0 0
#> chr8:27125591_C_G 0 0 0 0 0
#> chr8:27125730_A_G 0 0 0 0 0
#> chr8:27125829_T_A 0 0 0 0 0
#> chr8:27126386_A_G 0 0 0 0 0
#> chr8:27126486_C_T 0 0 0 0 0
#> chr8:27127215_T_A 0 0 0 0 0
#> chr8:27127370_T_C 0 0 0 0 0
#> chr8:27127374_T_C 0 0 0 0 0
#> chr8:27127405_T_C 0 0 0 0 0
#> chr8:27128069_G_A 0 0 0 0 0
#> chr8:27128102_T_TAAAG 0 0 0 0 0
#> chr8:27128473_C_G 0 0 0 0 0
#> chr8:27128733_G_T 0 0 0 0 0
#> chr8:27129375_G_GA 0 0 0 0 0
#> chr8:27129602_T_C 0 0 0 0 0
#> chr8:27129674_A_G 0 0 0 0 0
#> chr8:27129849_TAAA_T 0 0 0 0 0
#> chr8:27129864_G_A 0 0 0 0 0
#> chr8:27129921_C_T 0 0 0 0 0
#> chr8:27130038_G_A 0 0 0 0 0
#> chr8:27130250_G_C 0 0 0 0 0
#> chr8:27130586_G_C 0 0 0 0 0
#> chr8:27130820_A_T 0 0 0 0 0
#> chr8:27131153_G_T 0 0 0 0 0
#> chr8:27131169_T_A 0 0 0 0 0
#> chr8:27131173_C_T 0 0 0 0 0
#> chr8:27131449_G_A 0 0 0 0 0
#> chr8:27131584_G_A 0 0 0 0 0
#> chr8:27132152_T_C 0 0 0 0 0
#> cond_6 cond_7
#> chr8:27119632_TA_T 5.180715e-04 1.826926e-21
#> chr8:27119646_A_AG -9.418167e-05 -2.643751e-21
#> chr8:27119646_A_G -1.526077e-04 4.434983e-21
#> chr8:27119788_C_T 2.160531e-05 -1.365110e-22
#> chr8:27119867_G_T 2.160531e-05 -1.365110e-22
#> chr8:27119961_G_T 5.346543e-04 2.343178e-21
#> chr8:27120636_C_T -9.029812e-05 -2.013491e-21
#> chr8:27120932_A_G 3.531336e-05 1.247397e-21
#> chr8:27121290_T_C -3.242028e-04 2.909755e-22
#> chr8:27121498_C_A -3.242028e-04 2.909755e-22
#> chr8:27121702_G_A 1.089555e-04 -6.736369e-21
#> chr8:27121936_A_G -1.526077e-04 4.434983e-21
#> chr8:27122117_CAA_C -1.669376e-04 4.613961e-21
#> chr8:27122117_CAAA_C 5.347964e-06 -7.430836e-23
#> chr8:27122139_A_C 4.897130e-04 -6.444835e-21
#> chr8:27122351_G_A -2.916208e-04 -1.110037e-20
#> chr8:27123070_G_C -7.994489e-04 7.374222e-22
#> chr8:27123164_C_T -1.978132e-03 2.197239e-20
#> chr8:27123274_T_TG 5.023109e-04 1.330963e-20
#> chr8:27123283_T_TTTTTGTTTTGTTTTG -5.610249e-04 -8.769943e-21
#> chr8:27123283_T_TTTTTGTTTTG 2.972137e-05 1.762141e-21
#> chr8:27123283_T_TTTTTGTTTTGTTTTGTTTTG -6.609647e-03 1.184489e-19
#> chr8:27123383_C_T -8.612532e-04 -4.220061e-20
#> chr8:27123630_G_C -7.510018e-04 1.755359e-20
#> chr8:27123806_T_C -8.612532e-04 -4.220061e-20
#> chr8:27124049_A_G -8.612532e-04 -4.220061e-20
#> chr8:27124126_T_C -9.029812e-05 -2.013491e-21
#> chr8:27124147_C_A -8.612532e-04 -4.220061e-20
#> chr8:27124381_A_G -7.031334e-06 7.409137e-22
#> chr8:27124644_G_A -1.526077e-04 4.434983e-21
#> chr8:27124683_C_T -9.029812e-05 -2.013491e-21
#> chr8:27125591_C_G -7.031334e-06 7.409137e-22
#> chr8:27125730_A_G -2.259705e-05 -1.138763e-21
#> chr8:27125829_T_A -2.427355e-06 1.030686e-22
#> chr8:27126386_A_G -4.267826e-04 -6.647219e-22
#> chr8:27126486_C_T -1.526077e-04 4.434983e-21
#> chr8:27127215_T_A -9.099366e-05 2.402780e-21
#> chr8:27127370_T_C 2.188138e-05 1.352585e-21
#> chr8:27127374_T_C 2.188138e-05 1.352585e-21
#> chr8:27127405_T_C -1.526077e-04 4.434983e-21
#> chr8:27128069_G_A -8.612532e-04 -4.220061e-20
#> chr8:27128102_T_TAAAG -9.840182e-04 1.412230e-20
#> chr8:27128473_C_G 3.043701e-04 -1.724206e-21
#> chr8:27128733_G_T -9.029812e-05 -2.013491e-21
#> chr8:27129375_G_GA -8.612532e-04 -4.220061e-20
#> chr8:27129602_T_C -9.452814e-04 8.719400e-22
#> chr8:27129674_A_G -8.612532e-04 -4.220061e-20
#> chr8:27129849_TAAA_T 3.977784e-04 7.241409e-21
#> chr8:27129864_G_A 2.476848e-04 4.360402e-21
#> chr8:27129921_C_T 9.236548e-05 -7.308417e-23
#> chr8:27130038_G_A 3.043701e-04 -1.724206e-21
#> chr8:27130250_G_C 1.853110e-05 1.753773e-22
#> chr8:27130586_G_C -8.612532e-04 -4.220061e-20
#> chr8:27130820_A_T -9.099366e-05 2.402780e-21
#> chr8:27131153_G_T -1.526077e-04 4.434983e-21
#> chr8:27131169_T_A 1.853110e-05 1.753773e-22
#> chr8:27131173_C_T 2.592752e-04 5.447103e-21
#> chr8:27131449_G_A 1.308575e-05 -8.268100e-23
#> chr8:27131584_G_A -8.612532e-04 -4.220061e-20
#> chr8:27132152_T_C -9.099366e-05 2.402780e-21
# }