Get Residualized Phenotypes

Residualize the per-context phenotype matrices against the per-context phenotype covariates and the genotype covariates, for one or more requested contexts.

Usage

getResidualizedPhenotypes(x, ...)

# S4 method for class 'QtlDataset'
getResidualizedPhenotypes(
  x,
  contexts,
  traitId = NULL,
  region = NULL,
  phenotypeCovariatesToResidualize = NULL,
  genotypeCovariatesToResidualize = NULL,
  residualizePhenotypeCovariates = TRUE,
  residualizeGenotypeCovariates = TRUE,
  residualizePhenotypeCovariatesFromPhenotypes = NULL,
  residualizeGenotypeCovariatesFromPhenotypes = NULL,
  naAction = c("keep", "drop", "impute"),
  covariateNaAction = c("impute", "drop"),
  outlierAction = c("keep", "drop"),
  outlierPvalThreshold = 0.001,
  ...
)

Arguments

x

A QtlDataset object.

...

Selection arguments: contexts (required), traitId, region, phenotypeCovariatesToRemove, genotypeCovariatesToRemove, and covariateNaAction ("impute", the default, mean-imputes missing covariate cells; "drop" removes samples with any missing covariate).

contexts

Character vector. Context(s) whose data to extract.

traitId

Character or NULL. Molecular trait / feature identifier to select; NULL matches all traits in the dataset.

region

Character (length 1, "chr:start-end") or NULL. Restrict variants to this region; NULL uses the full cis window / all regions.

phenotypeCovariatesToResidualize

Character vector or NULL. Phenotype covariate names to residualize; NULL uses the dataset default set.

genotypeCovariatesToResidualize

Character vector or NULL. Genotype covariate names to residualize; NULL uses the dataset default set.

residualizePhenotypeCovariates

Logical. Whether to residualize the phenotype covariates. Default TRUE.

residualizeGenotypeCovariates

Logical. Whether to residualize the genotype covariates. Default TRUE.

residualizePhenotypeCovariatesFromPhenotypes

Logical or NULL. Whether to residualize phenotype covariates out of the phenotype; NULL uses the default.

residualizeGenotypeCovariatesFromPhenotypes

Logical or NULL. Whether to residualize genotype covariates out of the phenotype; NULL uses the default.

naAction

Character. How to handle missing phenotype values: one of "keep", "drop", or "impute".

covariateNaAction

Character. How to handle missing covariate values.

outlierAction

Character. How to handle phenotype outliers: one of "keep" or "drop".

outlierPvalThreshold

Numeric. Two-sided p-value threshold for flagging phenotype outliers. Default 1e-3.

Value

A named list of numeric matrices keyed by context.

Examples

data(qtlDatasetExample)
getResidualizedPhenotypes(qtlDatasetExample, contexts = "brain")
#>         ENSG_example
#> NA06989   0.07167318
#> NA11891   2.75786526
#> NA11843   0.47197104
#> NA12341   2.47442915
#> NA12739   1.36411662
#> NA10850  -1.71736462
#> NA06984   0.20969721
#> NA12877  -0.44452772
#> NA12275   1.26848404
#> NA06986  -0.41315456
#> NA12272   0.24394256
#> NA10845   0.95715294
#> NA10852  -0.18384509
#> NA07051   0.37188489
#> NA12400   0.01301770
#> NA12344  -0.34435438
#> NA12777  -1.18499697
#> NA12287  -1.15480963
#> NA10837   0.39870441
#> NA12383   0.42995429
#> NA12340   0.84008879
#> NA12708   1.66686907
#> NA12273  -0.27270854
#> NA11892  -2.43893341
#> NA12546  -0.30699370
#> NA12843   0.70294387
#> NA12766   2.04979578
#> NA12348   0.68359018
#> NA12817  -0.62560855
#> NA10840  -0.87667670
#> NA06997   1.52468124
#> NA11917  -0.33125604
#> NA12718  -0.51886700
#> NA12282   0.71148839
#> NA11920   1.17037107
#> NA12776  -0.25043657
#> NA12283   0.27096527
#> NA07435   0.24885197
#> NA12828  -1.93102973
#> NA07045   1.10393016
#> NA07031  -0.70813492
#> NA12336   0.28582678
#> NA07349   0.83604578
#> NA12827  -1.54396356
#> NA12375   0.09773920
#> NA12343  -0.90723342
#> NA12335   1.23967723
#> NA12778  -0.19124943
#> NA12832   0.81891538
#> NA11930  -0.65548341
#> NA12890   0.34362842
#> NA07037  -2.03656760
#> NA07347   1.55015479
#> NA12829   0.84243449
#> NA12749   0.03116427
#> NA11894  -0.20565526
#> NA12286   0.49752754
#> NA10865  -1.09225798
#> NA10864  -0.46465159
#> NA10853  -1.50005081
#> NA11918   0.65693527
#> NA12830  -0.17828262
#> NA12818  -0.91663891
#> NA10836   0.89334627
#> NA11893  -0.72699886
#> NA11919   0.71393524
#> NA12489   0.33433783
#> NA12399  -0.23909673
#> NA12413  -0.65967337
#> NA10843  -0.81602854
#> NA12842  -0.02012843
#> NA12347   2.50658029
#> NA07346   0.06612011
#> NA12775   0.08086174
#> NA07014  -1.62120299
#> NA12767  -0.32605859
#> NA12889   0.99002830
#> NA12386  -0.05053963
#> NA06995  -0.64696644
#> NA12376  -0.65870262
#> NA12342  -0.44568155
#> NA12748   0.12752562
#> NA11931   0.28810277
#> NA12045   0.35141511
#> NA12750  -1.46178759
#> NA11831  -0.27036485
#> NA12146   1.36769655
#> NA11882   0.70570055
#> NA07056  -0.77440301
#> NA12707   0.29918713
#> NA12154  -0.11189399
#> NA12753  -0.33852331
#> NA11839  -1.77417239
#> NA10859  -0.51293970
#> NA12875  -1.01876662
#> NA07348   0.97779868
#> NA12156   1.98134506
#> NA12044   0.41292860
#> NA11992  -0.44276672
#> NA11829  -0.13874363
#> NA12239  -0.54262360
#> NA12762   1.41869222
#> NA12716  -1.87801686
#> NA12878  -0.54898996
#> NA10856  -0.57746518
#> NA12874  -0.20439765
#> NA12760  -0.41621311
#> NA06985  -0.70558901
#> NA12003  -0.39320620
#> NA10835   0.38326654
#> NA07022  -0.25259164
#> NA12813   1.36834132
#> NA10839   0.73308873
#> NA07055  -0.88839305
#> NA12056  -0.16451663
#> NA10863   0.60963297
#> NA12145   1.39650374
#> NA12814   1.70629143
#> NA10847   0.02578332
#> NA12006  -0.53344399
#> NA12763  -0.52548356
#> NA07357   0.29950163
#> NA12144   1.02502559
#> NA10831  -0.51368002
#> NA07000  -1.02432345
#> NA11832  -0.98329113
#> NA06991  -0.01080641
#> NA11840   1.14028778
#> NA12802   0.80116324
#> NA12761   0.94938720
#> NA10830  -1.92545420
#> NA10855  -0.95041393
#> NA06994   0.78382906
#> NA11993   0.79148009
#> NA11995  -0.89932611
#> NA12891  -0.22183703
#> NA12864   0.27199723
#> NA12751  -1.52545998
#> NA10861   0.86969632
#> NA12005  -0.95431882
#> NA12234   0.31260681
#> NA07345   0.68199047
#> NA07029  -0.74462130
#> NA12892  -0.13958898
#> NA12248   0.55939301
#> NA10846   3.56972082
#> NA12801  -0.17727323
#> NA12872  -0.96576636
#> NA12155  -0.56506454
#> NA06993  -0.20279664
#> NA11830   1.15774856
#> NA10838  -0.88536055
#> NA12249  -1.65717467
#> NA12057  -0.88198305
#> NA12812  -0.31398374
#> NA11881  -0.26358421
#> NA11994  -0.57094114
#> NA12873  -1.70000858
#> NA12815  -1.38137291
#> NA12740  -0.19237917
#> NA12752   1.34989954
#> NA12043  -0.28515058
#> NA12264   1.21112749
#> NA10854  -0.04540513
#> NA12865  -0.65641461