Apply threshold filtering to a data frame — filter

This function applies threshold filtering to a data frame, summing values below the threshold for each column, storing the sum in the new 'Other' row, but only if all values within a row (taxon) across all columns are below the threshold.

Usage

filter_threshold(df, threshold, merged_profiles = TRUE)

Arguments

df: The input data frame of merged MetaPhlAn profiles.
threshold: The threshold value for filtering.
merged_profiles: Logical; if TRUE (the default) the file to be loaded is assumed to be multiple merged MetaPhlAn profiles.

Value

The filtered data frame.

Details

Function can be applied to a single MetaPhlAn profile by setting merged_profiles = FALSE. Likewise also works with merged profiles by slicing the data frame to only the clade_name and the numeric sample column of interest. In both cases a clade_name column is required.

Author

Jérémy Rotzetter

Examples

df <- data.frame(
  clade_name = c("A", "B", "C", "D"),
  col1 = c(10, 20, 5, 65),
  col2 = c(8, 15, 3, 38),
  col3 = c(5, 35, 4, 6)
)
print(df)
#>   clade_name col1 col2 col3
#> 1          A   10    8    5
#> 2          B   20   15   35
#> 3          C    5    3    4
#> 4          D   65   38    6
df_thresh <- filter_threshold(df, 11)
print(df_thresh)
#>   clade_name col1 col2 col3
#> 1          B   20   15   35
#> 2          D   65   38    6
#> 3      Other   15   11    9