downloadSequenceMetadata: Download Sequence Metadata

In claraqin/neonMicrobe: Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data

Download Sequence Metadata

Description

Loads soil marker gene sequencing metadata for specified target gene, site(s) and date(s), with an option to download output by providing a valid output directory. This function uses loadByProduct to conduct the downloads.

Usage

downloadSequenceMetadata(
  sites = "all",
  startYrMo = NA,
  endYrMo = NA,
  targetGene = "all",
  sequencingRuns = "",
  dpID = "DP1.10108.001",
  outDir = NULL
)

Arguments

sites	Either the string 'all', meaning all available sites, or a character vector of 4-letter NEON site codes, e.g. c('ONAQ','RMNP'). Defaults to PRESET_SITES parameter in params.R.
startYrMo, endYrMo	Either NA (default), meaning all available dates, or a character vector in the form YYYY-MM, e.g. 2017-01.
targetGene	'16S' or 'ITS'.
sequencingRuns	Either the string 'all', meaning all available sequencing runs, or a character vector of NEON sequencing run IDs, e.g. c('C25G9', 'B69PP').
dpID	NEON data product of interest. Default is soil marker gene sequences, and currently code only works for marker genes data products.
outDir	Directory where a copy of the downloaded data will be saved. By default (NULL), this is file.path(NEONMICROBE_DIR_SEQMETA(), "raw_metadata"). If no copy should be saved, set outDir=FALSE.

Details

Function by Lee F. Stanish and Clara Qin (2020). Currently available for testing only.

Value

Data frame containing joined records from across the NEON soil marker gene sequence metadata, subsetted according to function arguments.

Examples

 {
meta_16s <- downloadSequenceMetadata(
  startYrMo = "2017-07", endYrMo = "2017-07",
  sites = c("KONZ", "CPER", "NOGP"),
  targetGene = "16S"
)

claraqin/neonMicrobe documentation built on April 11, 2024, 11:47 a.m.