Normalize intensities across samples using grouped Quantile Normalization

This function performs a Quantile Normalization on each sub-group in the data set. It therefore requires grouping information. See Examples for more information. This approach might perform better than the standard approach, normalize_quantile_all, if sub-groups are very different (e.g., when comparing cancer vs. normal tissue).

Other sub-flavors are also available:

See References for more information. Note that it is equivalent to the 'Class-specific' normalization in Zhao et al. but has been renamed for internal consistency.

Usage

normalize_quantile_group(data, group_column = .data$Group)

Arguments

data: A tidy tibble created by read_featuretable.
group_column: Which column should be used for grouping? Usually grouping_column = Group. Uses args_data_masking.

Value

A tibble with intensities normalized across samples.

References

Y. Zhao, L. Wong, W. W. B. Goh, Sci Rep 2020, 10, 15534, DOI 10.1038/s41598-020-72664-6.

Examples

toy_metaboscape %>%
  # Metadata, including grouping information, must be added before using normalize_quantile_group()
  join_metadata(toy_metaboscape_metadata) %>%
  normalize_quantile_group(group_column = Group)
#> # A tibble: 110 × 12
#>      UID Feature      Sample Intensity    RT `m/z` Name  Formula Group Replicate
#>    <int> <chr>        <chr>      <dbl> <dbl> <dbl> <chr> <chr>   <chr>     <int>
#>  1     1 161.10519 D… Sampl…      3.83  0.45  162. NA    C7H15N… cont…         1
#>  2     2 276.13647 D… Sampl…      2.33  0.45  277. Octy… C16H22… cont…         1
#>  3     3 304.24023 D… Sampl…      8     0.55  305. Arac… C20H32… cont…         1
#>  4     4 417.23236 D… Sampl…      5.22  1     418. NA    NA      cont…         1
#>  5     5 104.10753 D… Sampl…      5.22  2.84  105. NA    C5H14NO cont…         1
#>  6     6 105.04259 D… Sampl…      5.22  3.33  106. NA    C3H8NO3 cont…         1
#>  7     7 237.09204 D… Sampl…    NaN     5.22  238. Keta… C13H16… cont…         1
#>  8     8 745.09111 D… Sampl…      2.33  6.37  746. NADPH C21H30… cont…         1
#>  9     9 427.02942 D… Sampl…      3.83  7.08  428. ADP   C10H15… cont…         1
#> 10    10 1284.34904 … Sampl…    NaN     8.32 1285. NA    NA      cont…         1
#> # ℹ 100 more rows
#> # ℹ 2 more variables: Batch <int>, Factor <dbl>