These functions return information about the most dominant taxa in a
SummarizedExperiment
object.
perSampleDominantFeatures(
x,
assay.type = assay_name,
assay_name = "counts",
rank = NULL,
other.name = "Other",
n = NULL,
complete = TRUE,
...
)
# S4 method for SummarizedExperiment
perSampleDominantFeatures(
x,
assay.type = assay_name,
assay_name = "counts",
rank = NULL,
other.name = "Other",
n = NULL,
complete = TRUE,
...
)
perSampleDominantTaxa(x, ...)
# S4 method for SummarizedExperiment
perSampleDominantTaxa(x, ...)
addPerSampleDominantFeatures(
x,
name = "dominant_taxa",
other.name = "Other",
n = NULL,
...
)
# S4 method for SummarizedExperiment
addPerSampleDominantFeatures(
x,
name = "dominant_taxa",
other.name = "Other",
n = NULL,
complete = FALSE,
...
)
addPerSampleDominantTaxa(x, ...)
# S4 method for SummarizedExperiment
addPerSampleDominantTaxa(x, ...)A
SummarizedExperiment
object.
A single character value for selecting the
assay
to use for identifying dominant taxa.
a single character value for specifying which
assay to use for calculation.
(Please use assay.type instead. At some point assay_name
will be disabled.)
A single character defining a taxonomic rank. Must be a value of
the output of taxonomyRanks().
A name for features that are not included in n the most frequent dominant features in the data. Default is "Other".
The number of features that are the most frequent dominant features. Default is NULL, which defaults that each sample is assigned a dominant taxon.
A boolean value to manage multiple dominant taxa for a sample. Default for perSampleDominantTaxa is TRUE to include all equally dominant taxa for each sample. complete = FALSE samples one taxa for the samples that have multiple. Default for addPerSampleDominantTaxa is FALSE to add a column with only one dominant taxon assigned for each sample into colData. complete = TRUE adds a list that includes all dominant taxa for each sample into colData.
Additional arguments passed on to agglomerateByRank() when
rank is specified.
A name for the column of the colData where the dominant
taxa will be stored in when using addPerSampleDominantFeatures.
perSampleDominantFeatures returns a named character vector x
while addPerSampleDominantFeatures returns
SummarizedExperiment
with additional column in colData named *name*.
addPerSampleDominantFeatures extracts the most abundant taxa in a
SummarizedExperiment
object, and stores the information in the colData. It is a wrapper for
perSampleDominantFeatures.
With rank parameter, it is possible to agglomerate taxa based on taxonomic
ranks. E.g. if 'Genus' rank is used, all abundances of same Genus are added
together, and those families are returned. See agglomerateByRank() for
additional arguments to deal with missing values or special characters.
data(GlobalPatterns)
x <- GlobalPatterns
# Finds the dominant taxa.
sim.dom <- perSampleDominantFeatures(x, rank="Genus")
# Add information to colData
x <- addPerSampleDominantFeatures(x, rank = "Genus", name="dominant_genera")
colData(x)
#> DataFrame with 26 rows and 8 columns
#> X.SampleID Primer Final_Barcode Barcode_truncated_plus_T
#> <factor> <factor> <factor> <factor>
#> CL3 CL3 ILBC_01 AACGCA TGCGTT
#> CC1 CC1 ILBC_02 AACTCG CGAGTT
#> SV1 SV1 ILBC_03 AACTGT ACAGTT
#> M31Fcsw M31Fcsw ILBC_04 AAGAGA TCTCTT
#> M11Fcsw M11Fcsw ILBC_05 AAGCTG CAGCTT
#> ... ... ... ... ...
#> TS28 TS28 ILBC_25 ACCAGA TCTGGT
#> TS29 TS29 ILBC_26 ACCAGC GCTGGT
#> Even1 Even1 ILBC_27 ACCGCA TGCGGT
#> Even2 Even2 ILBC_28 ACCTCG CGAGGT
#> Even3 Even3 ILBC_29 ACCTGT ACAGGT
#> Barcode_full_length SampleType
#> <factor> <factor>
#> CL3 CTAGCGTGCGT Soil
#> CC1 CATCGACGAGT Soil
#> SV1 GTACGCACAGT Soil
#> M31Fcsw TCGACATCTCT Feces
#> M11Fcsw CGACTGCAGCT Feces
#> ... ... ...
#> TS28 GCATCGTCTGG Feces
#> TS29 CTAGTCGCTGG Feces
#> Even1 TGACTCTGCGG Mock
#> Even2 TCTGATCGAGG Mock
#> Even3 AGAGAGACAGG Mock
#> Description dominant_genera
#> <factor> <character>
#> CL3 Calhoun South Carolina Pine soil, pH 4.9 Genus:CandidatusSoli..
#> CC1 Cedar Creek Minnesota, grassland, pH 6.1 Genus:MC18
#> SV1 Sevilleta new Mexico, desert scrub, pH 8.3 Class:Chloracidobact..
#> M31Fcsw M3, Day 1, fecal swab, whole body study Genus:Bacteroides
#> M11Fcsw M1, Day 1, fecal swab, whole body study Genus:Bacteroides
#> ... ... ...
#> TS28 Twin #1 Genus:Faecalibacterium
#> TS29 Twin #2 Family:Ruminococcaceae
#> Even1 Even1 Genus:Bacteroides
#> Even2 Even2 Genus:Bacteroides
#> Even3 Even3 Genus:Bacteroides