R/biomfiles_to_metabarlist.R
biomfiles_to_metabarlist.RdImports and formats BIOM and associated files to create a metabarlist object.
biomfiles_to_metabarlist(
file_biom,
file_samples,
file_pcrs = NULL,
file_motus = NULL,
...
)path for the BIOM file. This is either a JSON formatted file
(biom file format version 1) or a HDF5 formatted file (BIOM file format
version 2 and 2.1), as described at http://biom-format.org/.
This file should include at least MOTUs abundance data.
It may also store MOTUs and/or PCRs attributes data.
Mandatory fields for MOTUs and PCRs attributes data are described below.
path for the sample characteristics table. The first column of this table should contain the sample names.
path for the PCRs characteristics table (e.g. tags, primers, plate wells, etc.),
if the BIOM file is missing these data. Mandatory fields:
(i) `sample_id`, i.e. the name of each sample. (ii) `type`,
i.e. the type of PCR; can be `sample` or `control`. (iii) `control_type`,
i.e. the type of control if applicable. Should be: 'NA' for samples,
`extraction` for extraction negative controls, `pcr` for pcr negative controls,
`sequencing` for sequencing negative controls (e.g. unused tag combinations),
and `positive` for positive controls. The first column of this table should
correspond to the names of the PCRs.
path for the MOTUs characteristics table (e.g. taxonomy, sequence, etc.),
if the BIOM file is missing these data. Rows of the table should
correspond to MOTUs, and the columns to their characteristics.
Mandatory fields: 'sequence', i.e. the most abundant sequence of the MOTU.
The first column of this table should contain MOTU names.
other arguments to be pasted from read.table.
a metabarlist object
This function imports a BIOM file and associated files into R to create a metabarlist object. Two files are required: a BIOM file, as well as a sample characteristics table. If the BIOM file does not contain PCRs and MOTUs attributes data, two other files containing these data are required. The files are imported in R, included into a list of class metabarlist with the metabarlist_generator function, and congruencies between all tables are tested with the check_metabarlist function.
check_metabarlist, metabarlist_generator,
obifiles_to_metabarlist, tabfiles_to_metabarlist,
or the biomformat package
# \donttest{
dir <- tempdir()
url = "https://raw.githubusercontent.com/metabaRfactory/metabaR_external_data/master/"
litiere_euk_reads_hdf5_file = "litiere_euk_reads_hdf5.biom"
litiere_euk_reads_hdf5_url = paste(url, litiere_euk_reads_hdf5_file, sep="")
litiere_euk_reads_hdf5_path <- file.path(dir, litiere_euk_reads_hdf5_file)
download.file(litiere_euk_reads_hdf5_url, litiere_euk_reads_hdf5_path)
litiere_euk_motus_file = "litiere_euk_motus.txt"
litiere_euk_motus_url = paste(url, litiere_euk_motus_file, sep="")
litiere_euk_motus_path <- file.path(dir, litiere_euk_motus_file)
download.file(litiere_euk_motus_url, litiere_euk_motus_path)
litiere_euk_pcrs_file = "litiere_euk_pcrs.txt"
litiere_euk_pcrs_url = paste(url, litiere_euk_pcrs_file, sep="")
litiere_euk_pcrs_path = file.path(dir, litiere_euk_pcrs_file)
download.file(litiere_euk_pcrs_url, litiere_euk_pcrs_path)
litiere_euk_samples_file = "litiere_euk_samples.txt"
litiere_euk_samples_url = paste(url, litiere_euk_samples_file, sep="")
litiere_euk_samples_path = file.path(dir, litiere_euk_samples_file)
download.file(litiere_euk_samples_url, litiere_euk_samples_path)
soil_euk <- biomfiles_to_metabarlist(
file_biom = litiere_euk_reads_hdf5_path,
file_motus = litiere_euk_motus_path,
file_pcrs = litiere_euk_pcrs_path,
file_samples = litiere_euk_samples_path,
sep = "\t")
# }