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Group-based feature filtering

Source: R/filters.R
filter_grouped_mv.Rd

Similar to filter_global_mv it filters features that are found in a specified number of samples. The key difference is that filter_grouped_mv() takes groups into consideration and therefore needs sample metadata. For example, if fraction = TRUE and min_found = 0.5, a feature must be found in at least 50 % of the samples of at least 1 group. It is very similar to the Filter features by occurrences in groups option in Bruker MetaboScape.

Usage

filter_grouped_mv(
  data,
  min_found = 0.5,
  group_column = .data$Group,
  fraction = TRUE
)

Arguments

data

A tidy tibble created by read_featuretable with added sample metadata. See ?create_metadata_skeleton for help.

min_found

Defines in how many samples of at least 1 group a Feature must be found not to be filtered out. If fraction == TRUE, a value between 0 and 1 (e.g., 0.5 if a Feature must be found in at least half the samples of at least 1 group). If fraction == FALSE the absolute maximum number of samples (e.g., 5 if a specific Feature must be found in at least 5 samples of at least 1 group).

group_column

Which column should be used for grouping? Usually group_column = Group. Uses args_data_masking.

fraction

Either TRUE or FALSE. Should min_found be the absolute number of samples or a fraction?

Value

A filtered tibble.

Examples

# A Feature must be found in all samples of at least 1 group.
toy_metaboscape %>%
  join_metadata(toy_metaboscape_metadata) %>%
  filter_grouped_mv(min_found = 1, group_column = Group)
#> # A tibble: 99 × 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…         4  0.45  162. NA    C7H15N… cont…         1
#>  2     2 276.13647 D… Sampl…         3  0.45  277. Octy… C16H22… cont…         1
#>  3     3 304.24023 D… Sampl…        NA  0.55  305. Arac… C20H32… cont…         1
#>  4     4 417.23236 D… Sampl…         5  1     418. NA    NA      cont…         1
#>  5     5 104.10753 D… Sampl…         5  2.84  105. NA    C5H14NO cont…         1
#>  6     6 105.04259 D… Sampl…         5  3.33  106. NA    C3H8NO3 cont…         1
#>  7     7 237.09204 D… Sampl…        NA  5.22  238. Keta… C13H16… cont…         1
#>  8     8 745.09111 D… Sampl…         3  6.37  746. NADPH C21H30… cont…         1
#>  9     9 427.02942 D… Sampl…         4  7.08  428. ADP   C10H15… cont…         1
#> 10     1 161.10519 D… Sampl…         3  0.45  162. NA    C7H15N… cont…         2
#> # ℹ 89 more rows
#> # ℹ 2 more variables: Batch <int>, Factor <dbl>