This function takes a matrix of predictors (X) and a list of TWAS
(transcriptome-wide association studies) weights (weightsList), and
calculates the predicted outcomes by multiplying X by each set of
weights in weightsList. The names of the elements in the output list
are derived from the names in weightsList, with "_weights" replaced by
"_predicted".
Arguments
- X
A matrix or data frame of predictors where each row is an observation and each column is a variable.
- weightsList
A list of numeric vectors representing the weights for each predictor. The names of the list elements should follow the pattern
[outcome]_weights, where[outcome]is the name of the outcome variable that the weights are associated with.
Value
A named list of numeric vectors, where each vector is the predicted
outcome for the corresponding set of weights in weightsList. The
names of the list elements are derived from the names in weightsList
by replacing "_weights" with "_predicted".
Examples
data(multiTraitData)
X <- multiTraitData$X[, 1:4]
colnames(X) <- sprintf("chr1:%d:A:G", 100L * (1:4))
twe <- twasWeightsRow(variantIds = sprintf("chr1:%d:A:G", 100L * (1:4)),
weights = rep(0.1, 4), cvResult = list(rsq = 0.5), standardized = FALSE)
tw <- TwasWeights(study = "s1", context = "brain", trait = "g1",
method = "susie", entry = list(twe))
twasPredict(X, tw)
#> $susie_predicted
#> [,1]
#> sample_001 -0.00784822
#> sample_002 -0.17379010
#> sample_003 0.03811986
#> sample_004 0.18281389
#> sample_005 0.18281389
#> sample_006 0.18281389
#> sample_007 -0.06939935
#> sample_008 0.03811986
#> sample_009 0.07529468
#> sample_010 -0.17379010
#> sample_011 0.18281389
#> sample_012 0.18281389
#> sample_013 -0.02909607
#> sample_014 0.01339963
#> sample_015 0.07529468
#> sample_016 0.07529468
#> sample_017 -0.00784822
#> sample_018 -0.31848413
#> sample_019 0.03811986
#> sample_020 -0.17379010
#> sample_021 0.18281389
#> sample_022 -0.17379010
#> sample_023 0.03811986
#> sample_024 -0.31848413
#> sample_025 -0.17379010
#> sample_026 0.18281389
#> sample_027 -0.17379010
#> sample_028 -0.17379010
#> sample_029 -0.02909607
#> sample_030 -0.31848413
#> sample_031 -0.00784822
#> sample_032 0.28720464
#> sample_033 -0.31848413
#> sample_034 0.20406174
#> sample_035 -0.02909607
#> sample_036 0.07529468
#> sample_037 -0.02909607
#> sample_038 -0.02909607
#> sample_039 -0.02909607
#> sample_040 -0.02909607
#> sample_041 -0.06939935
#> sample_042 0.18281389
#> sample_043 0.07529468
#> sample_044 -0.02909607
#> sample_045 0.18281389
#> sample_046 0.18281389
#> sample_047 0.39472385
#> sample_048 -0.02909607
#> sample_049 -0.02909607
#> sample_050 -0.17379010
#> sample_051 -0.02909607
#> sample_052 -0.17379010
#> sample_053 0.18281389
#> sample_054 0.18281389
#> sample_055 -0.02909607
#> sample_056 -0.17379010
#> sample_057 0.18281389
#> sample_058 0.03811986
#> sample_059 0.03811986
#> sample_060 -0.17379010
#> sample_061 -0.06939935
#> sample_062 -0.17379010
#> sample_063 -0.17379010
#> sample_064 -0.00784822
#> sample_065 -0.06939935
#> sample_066 -0.17379010
#> sample_067 0.03811986
#> sample_068 -0.06939935
#> sample_069 0.07529468
#> sample_070 0.18281389
#> sample_071 0.18281389
#> sample_072 -0.17379010
#> sample_073 -0.17379010
#> sample_074 0.28720464
#> sample_075 0.18281389
#> sample_076 0.07529468
#> sample_077 0.03811986
#> sample_078 -0.00784822
#> sample_079 0.18281389
#> sample_080 -0.17379010
#> sample_081 -0.17379010
#> sample_082 0.03811986
#> sample_083 -0.17379010
#> sample_084 -0.31848413
#> sample_085 -0.02909607
#> sample_086 -0.17379010
#> sample_087 -0.17379010
#> sample_088 -0.02909607
#> sample_089 0.28720464
#> sample_090 -0.17379010
#> sample_091 0.18281389
#> sample_092 -0.02909607
#> sample_093 0.18281389
#> sample_094 0.07529468
#> sample_095 -0.02909607
#> sample_096 0.07529468
#> sample_097 0.07529468
#> sample_098 -0.02909607
#> sample_099 0.03811986
#> sample_100 -0.17379010
#> sample_101 0.07529468
#> sample_102 0.18281389
#> sample_103 0.03811986
#> sample_104 0.28720464
#> sample_105 -0.31848413
#> sample_106 -0.02909607
#> sample_107 -0.17379010
#> sample_108 0.07529468
#> sample_109 0.07529468
#> sample_110 -0.17379010
#> sample_111 0.03811986
#> sample_112 -0.17379010
#> sample_113 -0.02909607
#> sample_114 -0.02909607
#> sample_115 0.18281389
#> sample_116 -0.02909607
#> sample_117 0.07529468
#> sample_118 -0.17379010
#> sample_119 -0.02909607
#> sample_120 -0.17379010
#> sample_121 0.03811986
#> sample_122 0.07529468
#> sample_123 0.18281389
#> sample_124 0.39472385
#> sample_125 0.18281389
#> sample_126 -0.15254225
#> sample_127 -0.31848413
#> sample_128 -0.02909607
#> sample_129 0.18281389
#> sample_130 -0.31848413
#> sample_131 0.18281389
#> sample_132 0.07529468
#> sample_133 -0.02909607
#> sample_134 -0.02909607
#> sample_135 -0.00784822
#> sample_136 0.07529468
#> sample_137 0.18281389
#> sample_138 -0.17379010
#> sample_139 -0.06939935
#> sample_140 -0.17379010
#> sample_141 -0.02909607
#> sample_142 0.52332712
#> sample_143 0.01339963
#> sample_144 0.20406174
#> sample_145 -0.31848413
#> sample_146 0.18281389
#> sample_147 -0.02909607
#> sample_148 -0.02909607
#> sample_149 -0.31848413
#> sample_150 -0.00784822
#> sample_151 -0.06939935
#> sample_152 0.07529468
#> sample_153 -0.02909607
#> sample_154 0.03811986
#> sample_155 0.39472385
#> sample_156 0.18281389
#> sample_157 0.20406174
#> sample_158 -0.06939935
#> sample_159 0.09654253
#> sample_160 -0.02909607
#> sample_161 -0.02909607
#> sample_162 -0.31848413
#> sample_163 0.07529468
#> sample_164 -0.02909607
#> sample_165 -0.02909607
#> sample_166 -0.17379010
#> sample_167 -0.17379010
#> sample_168 -0.02909607
#> sample_169 0.18281389
#> sample_170 0.39472385
#> sample_171 0.03811986
#> sample_172 0.07529468
#> sample_173 -0.02909607
#> sample_174 -0.17379010
#> sample_175 0.17968544
#> sample_176 -0.02909607
#> sample_177 -0.17379010
#> sample_178 0.03811986
#> sample_179 -0.17379010
#> sample_180 0.20406174
#> sample_181 -0.02909607
#> sample_182 0.07529468
#> sample_183 -0.00784822
#> sample_184 -0.17379010
#> sample_185 0.18281389
#> sample_186 -0.17379010
#> sample_187 0.18281389
#> sample_188 0.18281389
#> sample_189 -0.31848413
#> sample_190 -0.17379010
#> sample_191 0.18281389
#> sample_192 -0.17379010
#> sample_193 0.18281389
#> sample_194 -0.02909607
#> sample_195 0.03811986
#> sample_196 0.28720464
#> sample_197 -0.31848413
#> sample_198 0.33266501
#> sample_199 0.18281389
#> sample_200 -0.02909607
#> sample_201 -0.00784822
#> sample_202 -0.31848413
#> sample_203 0.09654253
#> sample_204 -0.00784822
#> sample_205 -0.02909607
#> sample_206 -0.17379010
#> sample_207 -0.17379010
#> sample_208 0.03811986
#> sample_209 -0.17379010
#> sample_210 0.07529468
#> sample_211 -0.02909607
#> sample_212 0.07529468
#> sample_213 0.03811986
#> sample_214 -0.02909607
#> sample_215 -0.06939935
#> sample_216 -0.02909607
#> sample_217 0.03811986
#> sample_218 -0.00784822
#> sample_219 -0.17379010
#> sample_220 0.09654253
#> sample_221 -0.15254225
#> sample_222 0.28720464
#> sample_223 -0.02909607
#> sample_224 0.17968544
#> sample_225 -0.02909607
#> sample_226 0.03811986
#> sample_227 0.07529468
#> sample_228 0.18281389
#> sample_229 -0.02909607
#> sample_230 -0.02909607
#> sample_231 0.18281389
#> sample_232 -0.02909607
#> sample_233 0.03811986
#> sample_234 -0.17379010
#> sample_235 0.07529468
#> sample_236 -0.17379010
#> sample_237 -0.02909607
#> sample_238 -0.17379010
#> sample_239 -0.31848413
#> sample_240 -0.02909607
#> sample_241 -0.02909607
#> sample_242 -0.06939935
#> sample_243 0.03811986
#> sample_244 -0.17379010
#> sample_245 -0.17379010
#> sample_246 0.18281389
#> sample_247 0.07529468
#> sample_248 -0.15254225
#> sample_249 0.07529468
#> sample_250 0.18281389
#> sample_251 0.52332712
#> sample_252 0.18281389
#> sample_253 0.18281389
#> sample_254 0.03811986
#> sample_255 0.03811986
#> sample_256 0.28720464
#> sample_257 -0.02909607
#> sample_258 0.20406174
#> sample_259 0.18281389
#> sample_260 -0.17379010
#> sample_261 -0.17379010
#> sample_262 -0.17379010
#> sample_263 -0.02909607
#> sample_264 -0.17379010
#> sample_265 0.18281389
#> sample_266 -0.02909607
#> sample_267 -0.02909607
#> sample_268 -0.02909607
#> sample_269 -0.17379010
#> sample_270 -0.00784822
#> sample_271 0.07529468
#> sample_272 -0.31848413
#> sample_273 -0.00784822
#> sample_274 0.18281389
#> sample_275 -0.31848413
#> sample_276 0.18281389
#> sample_277 -0.00784822
#> sample_278 -0.17379010
#> sample_279 -0.02909607
#> sample_280 -0.17379010
#> sample_281 -0.02909607
#> sample_282 -0.31848413
#> sample_283 -0.02909607
#> sample_284 -0.02909607
#> sample_285 0.18281389
#> sample_286 -0.31848413
#> sample_287 0.39472385
#> sample_288 0.28720464
#> sample_289 0.07529468
#> sample_290 -0.02909607
#> sample_291 -0.06939935
#> sample_292 -0.06939935
#> sample_293 -0.02909607
#> sample_294 -0.06939935
#> sample_295 -0.02909607
#> sample_296 0.18281389
#> sample_297 -0.17379010
#> sample_298 0.07529468
#> sample_299 0.18281389
#> sample_300 -0.02909607
#> sample_301 -0.17379010
#> sample_302 0.18281389
#> sample_303 -0.15254225
#> sample_304 -0.02909607
#> sample_305 0.07529468
#> sample_306 -0.15254225
#> sample_307 0.07529468
#> sample_308 -0.00784822
#> sample_309 0.20406174
#> sample_310 -0.31848413
#> sample_311 0.07529468
#> sample_312 -0.17379010
#> sample_313 -0.17379010
#> sample_314 -0.02909607
#> sample_315 0.18281389
#> sample_316 0.09654253
#> sample_317 -0.31848413
#> sample_318 -0.17379010
#> sample_319 -0.06939935
#> sample_320 -0.00784822
#> sample_321 -0.17379010
#> sample_322 0.07529468
#> sample_323 -0.17379010
#> sample_324 0.18281389
#> sample_325 0.20406174
#> sample_326 -0.02909607
#> sample_327 -0.02909607
#> sample_328 -0.02909607
#> sample_329 0.18281389
#> sample_330 0.20406174
#> sample_331 0.20406174
#> sample_332 0.07529468
#> sample_333 0.07529468
#> sample_334 -0.02909607
#> sample_335 -0.17379010
#> sample_336 0.39472385
#> sample_337 0.18281389
#> sample_338 0.28720464
#> sample_339 0.03811986
#> sample_340 -0.02909607
#> sample_341 0.18281389
#> sample_342 -0.02909607
#> sample_343 -0.17379010
#> sample_344 -0.17379010
#> sample_345 0.07529468
#> sample_346 -0.02909607
#> sample_347 -0.06939935
#> sample_348 -0.06939935
#> sample_349 0.03811986
#> sample_350 0.07529468
#> sample_351 -0.17379010
#> sample_352 0.18281389
#> sample_353 -0.17379010
#> sample_354 -0.17379010
#> sample_355 0.03811986
#> sample_356 -0.17379010
#> sample_357 0.03811986
#> sample_358 0.03811986
#> sample_359 -0.02909607
#> sample_360 0.07529468
#> sample_361 -0.17379010
#> sample_362 0.18281389
#> sample_363 -0.17379010
#> sample_364 -0.17379010
#> sample_365 0.28720464
#> sample_366 -0.17379010
#> sample_367 -0.17379010
#> sample_368 0.03811986
#> sample_369 -0.02909607
#> sample_370 -0.17379010
#> sample_371 0.39472385
#> sample_372 -0.17379010
#> sample_373 0.03811986
#> sample_374 0.18281389
#> sample_375 -0.02909607
#> sample_376 -0.17379010
#> sample_377 -0.02909607
#> sample_378 -0.17379010
#> sample_379 0.28720464
#> sample_380 -0.17379010
#> sample_381 -0.17379010
#> sample_382 0.18281389
#> sample_383 -0.00784822
#> sample_384 0.18281389
#> sample_385 -0.18988086
#> sample_386 -0.02909607
#> sample_387 -0.02909607
#> sample_388 -0.17379010
#> sample_389 -0.17379010
#> sample_390 -0.17379010
#> sample_391 -0.31848413
#> sample_392 0.18281389
#> sample_393 -0.00784822
#> sample_394 -0.02909607
#> sample_395 0.39472385
#> sample_396 0.18281389
#> sample_397 -0.00784822
#> sample_398 -0.02909607
#> sample_399 0.18281389
#> sample_400 0.20406174
#>