Scale intensities of features using level scaling

Scales the intensities of all features using

$$\widetilde{x}_{ij}=\frac{x_{ij}-\overline{x}_{i}}{\overline{x}_{i}}$$

where \(\widetilde{x}_{ij}\) is the intensity of sample \(j\), feature \(i\) after scaling, \(x_{ij}\) is the intensity of sample \(j\), feature \(i\) before scaling and \(\overline{x}_{i}\) is the mean of intensities of feature \(i\) across all samples

In other words, it performs centering (scale_center) and divides by the feature mean, thereby focusing on the relative intensity.

Usage

scale_level(data)

Arguments

data

A tidy tibble created by read_featuretable.

Value

A tibble with level scaled intensities.

References

• R. A. Van Den Berg, H. C. Hoefsloot, J. A. Westerhuis, A. K. Smilde, M. J. Van Der Werf, BMC Genomics 2006, 7, 142, DOI 10.1186/1471-2164-7-142.

Examples

toy_metaboscape %>%
  impute_lod() %>%
  scale_level()
#> # 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   -0.0393  0.45  162. NA         C7H15N…
#>  2     2 276.13647 Da 27.28 s   Sample1   -0.377   0.45  277. Octyl hyd… C16H22…
#>  3     3 304.24023 Da 32.86 s   Sample1   -0.948   0.55  305. Arachidon… C20H32…
#>  4     4 417.23236 Da 60.08 s   Sample1   -0.0709  1     418. NA         NA     
#>  5     5 104.10753 Da 170.31 s  Sample1    0.217   2.84  105. NA         C5H14NO
#>  6     6 105.04259 Da 199.80 s  Sample1    0.297   3.33  106. NA         C3H8NO3
#>  7     7 237.09204 Da 313.24 s  Sample1   -0.575   5.22  238. Ketamine   C13H16…
#>  8     8 745.09111 Da 382.23 s  Sample1    0.260   6.37  746. NADPH      C21H30…
#>  9     9 427.02942 Da 424.84 s  Sample1   -0.0265  7.08  428. ADP        C10H15…
#> 10    10 1284.34904 Da 498.94 s Sample1   -0.667   8.32 1285. NA         NA     
#> # ℹ 100 more rows