/usr/lib/R/site-library/biomformat/doc/biomformat.R is in r-bioc-biomformat 1.2.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | ## ----packages------------------------------------------------------------
library("biomformat"); packageVersion("biomformat")
## ----read-biom-examples--------------------------------------------------
min_dense_file = system.file("extdata", "min_dense_otu_table.biom",
package = "biomformat")
min_sparse_file = system.file("extdata", "min_sparse_otu_table.biom",
package = "biomformat")
rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom",
package = "biomformat")
rich_sparse_file = system.file("extdata", "rich_sparse_otu_table.biom",
package = "biomformat")
min_dense_file = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat")
rich_dense_char = system.file("extdata", "rich_dense_char.biom", package = "biomformat")
rich_sparse_char = system.file("extdata", "rich_sparse_char.biom", package = "biomformat")
x1 = read_biom(min_dense_file)
x2 = read_biom(min_sparse_file)
x3 = read_biom(rich_dense_file)
x4 = read_biom(rich_sparse_file)
x5 = read_biom(rich_dense_char)
x6 = read_biom(rich_sparse_char)
x1
## ----accessor-examples-table---------------------------------------------
biom_data(x1)
biom_data(x2)
## ----matrix-coercion-----------------------------------------------------
as(biom_data(x2), "matrix")
## ----observ-meta---------------------------------------------------------
observation_metadata(x1)
observation_metadata(x2)
observation_metadata(x3)
observation_metadata(x4)[1:2, 1:3]
class(observation_metadata(x4))
## ----plot-examples-------------------------------------------------------
sample_metadata(x1)
sample_metadata(x2)
sample_metadata(x3)
sample_metadata(x4)[1:2, 1:3]
class(sample_metadata(x4))
## ----plot----------------------------------------------------------------
plot(biom_data(x4))
boxplot(as(biom_data(x4), "vector"))
heatmap(as(biom_data(x4), "matrix"))
## ----write-biom-examples-------------------------------------------------
outfile = tempfile()
write_biom(x4, outfile)
y = read_biom(outfile)
identical(x4, y)
## ----compare-files-diff, eval=FALSE--------------------------------------
# # On Unix OSes
# system(paste0("diff ", rich_sparse_file, outfile))
# # On windows
# system(paste0("FC ", rich_sparse_file, outfile))
|