Basically a wrapper function around missForest::missForest. Imputes missing values using the random forest algorithm.
Arguments
- data
A tidy tibble created by
read_featuretable.- random_seed
A seed for the random number generator. Can be an integer or
NULL(in case no particular seed should be used) but for reproducibility reasons it is strongly advised to provide an integer.- ...
Additional parameters passed to
missForest.
References
missForest on CRAN
D. J. Stekhoven, P. Bühlmann, Bioinformatics 2012, 28, 112–118, DOI 10.1093/bioinformatics/btr597.
Examples
toy_metaboscape %>%
impute_rf()
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> Warning: The response has five or fewer unique values. Are you sure you want to do regression?
#> # 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 5.25 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 8.2 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 3.23 8.32 1285. NA NA
#> # ℹ 100 more rows