microbio_me_qiime: Import microbio.me/qiime (QIIME-DB) data package

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Import microbio.me/qiime (QIIME-DB) data package

Description

Originally, this function was for accessing microbiome datasets from the microbio.me/qiime public repository from within R. As you can see by clicking on the above link, the QIIME-DB sever is down indefinitely. However, this function will remain supported here in case the FTP server goes back up, and also for phyloseq users that have downloaded one or more data packages prior to the server going down.

Usage

microbio_me_qiime(zipftp, ext = ".zip",
  parsef = parse_taxonomy_greengenes, ...)

Arguments

zipftp	(Required). A character string that is the full URL path to a zipped file that follows the file naming conventions used by microbio.me/qiime. Alternatively, you can simply provide the study number as a single integer or other single-length vector that can be coerced to an integer; this function will complete the remainder of the ftp URL hosted at microbio.me/qiime. For example, instead of the full URL string, "ftp://thebeast.colorado.edu/pub/QIIME_DB_Public_Studies/study_494_split_library_seqs_and_mapping.zip", you could simply provide 494 or "494" as the first ('zipftp') argument.
ext	(Optional). A character string of the expected file extension, which also indicates the compression type, if zipftp is a study number instead of the full path. Note that this argument has no effect if zipftp is the full path, in which case the file extension is read directly from the downloaded file.
parsef	(Optional). The type of taxonomic parsing to use for the OTU taxonomic classification, in the .biom file, if present. This is passed on to import_biom, but unlike that function the default parsing function is parse_taxonomy_greengenes, rather than parse_taxonomy_default, because we know ahead of time that most (or all?) of the taxonomic classifications in the microbio.me/qiime repository will be based on GreenGenes.
...	(Optional, for advanced users). Additional arguments passed to download.file. This is mainly for non-standard links to resources (in this case, a zipped file) that are not being hosted by microbio.me/qiime. If you are using a FTP address or study number from their servers, then you shouldn't need to provide any additional arguments.

Value

A phyloseq-class object if possible, a component if only a component could be imported, or NULL if nothing could be imported after unzipping the file. Keep in mind there is a specific naming-convention that is expected based on the current state of the microbio.me/qiime servers. Several helpful messages are catted to standard out to help let you know the ongoing status of the current download and import process.

See Also

See download.file and url for details about URL formats – including local file addresses – that might work here.

import_biom

import_qiime

Examples

# This should return TRUE on your system if you have internet turned on
# and a standard R installation. Indicates whether this is likely to
# work on your system for a URL or local file, respectively.
capabilities("http/ftp"); capabilities("fifo")
# A working example with a local example file included in phyloseq
zipfile = "study_816_split_library_seqs_and_mapping.zip"
zipfile = system.file("extdata", zipfile, package="phyloseq")
tarfile = "study_816_split_library_seqs_and_mapping.tar.gz"
tarfile = system.file("extdata", tarfile, package="phyloseq")
tarps = microbio_me_qiime(tarfile)
zipps = microbio_me_qiime(zipfile) 
identical(tarps, zipps)
tarps; zipps
plot_heatmap(tarps)
# An example that used to work, before the QIIME-DB server was turned off by its host.
# # Smokers dataset
# smokezip = "ftp://thebeast.colorado.edu/pub/QIIME_DB_Public_Studies/study_524_split_library_seqs_and_mapping.zip"
# smokers1 = microbio_me_qiime(smokezip)
# # Alternatively, just use the study number
# smokers2 = microbio_me_qiime(524)
# identical(smokers1, smokers2)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.