Only keep shared samples between metadata and MetaPhlAn profile — clean

The clean_metadata() function is designed to clean and prepare metadata and a MetaPhlAn profile for further analysis by only keeping shared samples.

Usage

clean_metadata(metadata, mtphlan_profile, sample_column, remove_spaces = TRUE)

Arguments

metadata: A data frame containing metadata information.
mtphlan_profile: A data frame containing metaphlan profile information. Samples are columns.
sample_column: A character string. The column in the metadata containing the sample names. Should match column names of the MetaPhlAn profile.
remove_spaces: Should spaces (" ") be replaced with "_" in the column names?

Value

The cleaned metadata as a data frame.

Author

Jérémy Rotzetter

Examples

metadata <- data.frame(
  Sample_name = c("A", "B", "C", "D", "F", "G"),
  Sex = c(rep(c("F", "M")))
)

mtphlan_profile <- data.frame(
  clade_name = c("x", "y", "z"),
  A = c(1, 2, 3),
  B = c(4, 5, 6),
  D = c(7, 8, 9),
  Z = c(10, 11, 12)
)

cleaned_metadata <- clean_metadata(metadata, mtphlan_profile, "Sample_name")
#> Metadata and profile Sample_names match.

print(cleaned_metadata)
#>   Sample_name Sex
#> 1           A   F
#> 2           B   M
#> 4           D   M