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Join multiple MetaPhlAn profiles

Source: R/metaphlanProfile-class.R
join_mpa_profiles.Rd

Combines multiple metaphlanProfile objects into a single profile by joining their taxonomic abundance tables on the clade_name column.

Usage

join_mpa_profiles(...)

Arguments

...

Multiple objects of class metaphlanProfile to merge.

Value

An object of class metaphlanProfile containing the merged taxonomic profiles. All input profiles must use the same MetaPhlAn database version.

Details

  • Non-metaphlanProfile arguments are silently dropped with a warning.

  • Profiles from different MetaPhlAn database versions will cause an error.

  • Numeric suffixes will automatically be added to duplicate samples (e.g. Sample_1 -> Sample_1.1, Sample_1.2).

  • Missing values (NA) after joining are replaced with 0.0.

Examples

if (FALSE) { # \dontrun{
mtp1 <- load_metaphlan("path/to/profile1.txt")
mtp2 <- load_metaphlan("path/to/profile2.txt")
merged_profile <- join_mpa_profiles(mtp1, mtp2)
} # }