Deprecated functions in package rbiom.
Source:R/rbiom-deprecated.r
, R/taxa_table.r
rbiom-deprecated.Rd
The functions listed below are deprecated and will be defunct in
the near future. When possible, alternative functions with similar
functionality are also mentioned. Help pages for deprecated functions are
available at help("<function>-deprecated")
.
Usage
alpha.div(biom, rarefy = FALSE)
beta.div(biom, method, weighted = TRUE, tree = NULL, long = FALSE, md = FALSE)
counts(biom)
info(biom)
metadata(biom, field = NULL, cleanup = FALSE)
nsamples(biom)
ntaxa(biom)
phylogeny(biom)
read.biom(src, tree = "auto", prune = FALSE)
read.fasta(file, ids = NULL)
read.tree(src)
sample.names(biom)
# S3 method for class 'rbiom'
select(
.data,
samples = NULL,
nTop = NULL,
nRandom = NULL,
seed = 0,
biom = NULL,
...
)
sequences(biom)
subtree(tree, tips)
taxa.names(biom)
taxa.ranks(biom)
taxa.rollup(
biom,
rank = "OTU",
map = NULL,
lineage = FALSE,
sparse = FALSE,
taxa = NULL,
long = FALSE,
md = FALSE
)
taxonomy(biom, ranks = NULL, unc = "asis")
tips(x)
unifrac(biom, weighted = TRUE, tree = NULL)
write.biom(biom, file, format = "json")
write.fasta(seqs, outfile = NULL)
write.tree(tree, file = NULL)
write.xlsx(biom, outfile, depth = NULL, seed = 0)
as.percent(biom)
comments(biom)
depth(biom)
depths_barplot(
biom,
rline = TRUE,
counts = TRUE,
labels = TRUE,
transform = "log10",
...
)
has.phylogeny(biom)
has.sequences(biom)
id(biom)
is.rarefied(biom)
read_biom(src, tree = "auto", ...)
repair(biom)
sample_subset(x, ...)
sample.sums(biom, long = FALSE, md = FALSE)
taxa.means(biom, rank = NULL)
taxa.sums(biom, rank = NULL)
top.taxa(biom, rank = "OTU", n = Inf)
top_taxa(biom, rank = "OTU", n = Inf)
comments(x) <- value
counts(x) <- value
id(x) <- value
metadata(x) <- value
phylogeny(x) <- value
sample.names(x) <- value
sequences(x) <- value
taxa.names(x) <- value
taxa.ranks(x) <- value
taxonomy(x) <- value
taxa_max(biom, rank = -1, lineage = FALSE, unc = "singly")
alpha.div
Use adiv_matrix()
or adiv_table()
instead.
beta.div
Use bdiv_table()
or bdiv_distmat()
instead.
read.biom
Use as_rbiom()
instead.
read.fasta
Use read_fasta()
instead.
read.tree
Use read_tree()
instead.
select
Use slice()
instead.
subtree
Use tree_subset()
instead.
taxa.rollup
Use taxa_table()
taxa_matrix()
instead.
unifrac
Use bdiv_distmat()
or bdiv_table()
instead.
write.biom
Use write_biom()
instead.
write.fasta
Use write_fasta()
instead.
write.tree
Use write_tree()
instead.
write.xlsx
Use write_xlsx()
instead.
depth
Use sample_sums()
instead.
depths_barplot
Use rare_stacked()
instead.
read_biom
Use as_rbiom()
instead.
sample.sums
Use sample_sums()
or adiv_table()
instead.
taxa.means
Use taxa_means()
instead.
taxa.sums
Use taxa_sums()
instead.
top.taxa
Use taxa_sums()
instead.
top_taxa
Use taxa_sums()
instead.