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Impute missing values using nearest neighbor averaging

Source: R/imputes.R
impute_knn.Rd

Basically a wrapper function around impute::impute.knn. Imputes missing values using the k-th nearest neighbor algorithm.

Note that the function ln-transforms the data prior to imputation and transforms it back to the original scale afterwards. Please do not do it manually prior to calling impute_knn()! See References for more information.

Important Note

impute_knn() depends on the impute package from Bioconductor. If metamorphr was installed via install.packages(), dependencies from Bioconductor were not automatically installed. When impute_knn() is called without the impute package installed, you should be asked if you want to install pak and impute. If you want to use impute_knn() you have to install those. In case you run into trouble with the automatic installation, please install impute manually. See impute: Imputation for microarray data for instructions on manual installation.

Usage

impute_knn(data, quietly = TRUE, ...)

Arguments

data

A tidy tibble created by read_featuretable.

quietly

TRUE or FALSE. Should messages and warnings from impute.knn be printed to the console?

...

Additional parameters passed to impute.knn.

Value

A tibble with imputed missing values.

References

  • Robert Tibshirani, Trevor Hastie, 2017, DOI 10.18129/B9.BIOC.IMPUTE.

  • J. Khan, J. S. Wei, M. Ringnér, L. H. Saal, M. Ladanyi, F. Westermann, F. Berthold, M. Schwab, C. R. Antonescu, C. Peterson, P. S. Meltzer, Nat Med 2001, 7, 673–679, DOI 10.1038/89044.

Examples

toy_metaboscape %>%
  impute_knn()
#> Warning: 2 rows with more than 50 % entries missing;
#>  mean imputation used for these rows
#> # A tibble: 110 × 8
#>      UID Feature                Sample  Intensity    RT `m/z` Name       Formula
#>    <int> <chr>                  <chr>       <dbl> <dbl> <dbl> <chr>      <chr>  
#>  1     1 161.10519 Da 26.98 s   Sample1      4     0.45  162. NA         C7H15N…
#>  2     2 276.13647 Da 27.28 s   Sample1      3     0.45  277. Octyl hyd… C16H22…
#>  3     3 304.24023 Da 32.86 s   Sample1      4.04  0.55  305. Arachidon… C20H32…
#>  4     4 417.23236 Da 60.08 s   Sample1      5     1     418. NA         NA     
#>  5     5 104.10753 Da 170.31 s  Sample1      5     2.84  105. NA         C5H14NO
#>  6     6 105.04259 Da 199.80 s  Sample1      5     3.33  106. NA         C3H8NO3
#>  7     7 237.09204 Da 313.24 s  Sample1      4.05  5.22  238. Ketamine   C13H16…
#>  8     8 745.09111 Da 382.23 s  Sample1      3     6.37  746. NADPH      C21H30…
#>  9     9 427.02942 Da 424.84 s  Sample1      4     7.08  428. ADP        C10H15…
#> 10    10 1284.34904 Da 498.94 s Sample1      4.05  8.32 1285. NA         NA     
#> # ℹ 100 more rows