Merge any number of ampvis2 objects into a single object.
amp_merge_ampvis2(
...,
by_refseq = TRUE,
refseq_names = NULL,
rename_unmatched = TRUE,
unmatched_prefix = "unmatched"
)(required) Any number of ampvis2-class objects to merge
(recommended) Merge by exact matches between DNA reference sequences. The full DNA sequences will then be used as the new names in the output. (default: TRUE)
Path to a FASTA file or a DNAbin class object with sequences whose names will be used as OTU names by exact matches (i.e. same length, 100% sequence identity). (default: NULL)
Whether to rename any unmatched sequences or not when refseq_names is provided. (default: TRUE)
Prefix used to name any unmatched sequences when refseq_names is provided. An integer counting from 1 will be appended to this prefix, so for example the 123th unmatched sequence will be named unmatched123, and so on. (default: "unmatched")
An ampvis2-class object
It's important to ensure that the taxonomy for all OTU's across data sets is generated in the exact same way with the same database.
When by_refseq = FALSE it's likewise important to ensure that OTU ID's are not arbitrary between data sets and that they are corresponding to the same sequences across data sets (objects).
When by_refseq = TRUE the full DNA sequences will be used as the new OTU ID's unless refseq_names is provided.
Currently, phylogenetic trees are not merged. Feel free to contribute.
data("MiDAS")
# summary of samples from 2010-2012
amp_filter_samples(
MiDAS,
Year %in% c("2010", "2011", "2012")
)
#> 488 samples and 2220 OTUs have been filtered
#> Before: 658 samples and 14969 OTUs
#> After: 170 samples and 12749 OTUs
#> ampvis2 object with 5 elements.
#> Summary of OTU table:
#> Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads
#> 170 12749 5308714 18373 42811 31385
#> Avg#Reads
#> 31227.73
#>
#> Assigned taxonomy:
#> Kingdom Phylum Class Order Family
#> 12749(100%) 12396(97.23%) 10987(86.18%) 9966(78.17%) 8631(67.7%)
#> Genus Species
#> 6566(51.5%) 26(0.2%)
#>
#> Metadata variables: 5
#> SampleID, Plant, Date, Year, Period
# now merge individual objects and verify summary is the same
d_2010 <- amp_filter_samples(
MiDAS,
Year %in% "2010"
)
#> 594 samples and 5022 OTUs have been filtered
#> Before: 658 samples and 14969 OTUs
#> After: 64 samples and 9947 OTUs
d_2011 <- amp_filter_samples(
MiDAS,
Year %in% "2011"
)
#> 610 samples and 4989 OTUs have been filtered
#> Before: 658 samples and 14969 OTUs
#> After: 48 samples and 9980 OTUs
d_2012 <- amp_filter_samples(
MiDAS,
Year %in% "2012"
)
#> 600 samples and 4127 OTUs have been filtered
#> Before: 658 samples and 14969 OTUs
#> After: 58 samples and 10842 OTUs
amp_merge_ampvis2(
d_2010,
d_2011,
d_2012
)
#> ampvis2 object with 5 elements.
#> Summary of OTU table:
#> Samples OTUs Total#Reads Min#Reads Max#Reads Median#Reads
#> 170 12749 5308714 18373 42811 31385
#> Avg#Reads
#> 31227.73
#>
#> Assigned taxonomy:
#> Kingdom Phylum Class Order Family
#> 12749(100%) 12396(97.23%) 10987(86.18%) 9966(78.17%) 8631(67.7%)
#> Genus Species
#> 6566(51.5%) 26(0.2%)
#>
#> Metadata variables: 5
#> SampleID, Plant, Date, Year, Period