Removes all OTUs that are not found with a higher relative abundance than the set threshold in percent in at least one sample.
filter_otus(data, filter_otus = 0)
filter_species(data, filter_otus = 0)(required) Data list as loaded with amp_load.
Remove low abundant OTU's across all samples below this threshold in percent. (default: 0)
An ampvis2 object
data("AalborgWWTPs")
AalborgWWTPs
#> ampvis2 object with 5 elements.
#> Summary of OTU table:
#> Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads
#> 67 9430 2045128 17772 44326 31209
#> Avg#Reads
#> 30524.3
#>
#> Assigned taxonomy:
#> Kingdom Phylum Class Order Family Genus
#> 9430(100%) 9215(97.72%) 8282(87.83%) 7644(81.06%) 6746(71.54%) 5228(55.44%)
#> Species
#> 23(0.24%)
#>
#> Metadata variables: 5
#> SampleID, Plant, Date, Year, Period
filtered <- filter_otus(AalborgWWTPs, filter_otus = 0.1)
#> 8628 OTUs not present in more than 0.1% relative abundance in any sample have been filtered
#> Before: 9430 OTUs
#> After: 802 OTUs
filtered
#> ampvis2 object with 5 elements.
#> Summary of OTU table:
#> Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads
#> 67 802 1763002 15601 38237 26515
#> Avg#Reads
#> 26313.46
#>
#> Assigned taxonomy:
#> Kingdom Phylum Class Order Family Genus
#> 802(100%) 793(98.88%) 755(94.14%) 742(92.52%) 709(88.4%) 584(72.82%)
#> Species
#> 3(0.37%)
#>
#> Metadata variables: 5
#> SampleID, Plant, Date, Year, Period