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Raw WIMP files plus metadata to metagenomeseq object

Source: R/wimp_raw_to_metagenomeseq.R
wimp_raw_to_metagenomeseq.Rd

Given WIMP directory and metadata, make phyloseq object. metagenomeSeq package required.

Usage

wimp_raw_to_metagenomeseq(
  path.to.wimp.files,
  metadata,
  keep.unclassified = FALSE,
  keep.human = FALSE
)

Arguments

path.to.wimp.files

path to data of raw CSV files from WIMP analysis

metadata

dataframe of metadata with "filename" and "barcode" columns required

keep.unclassified

TRUE or FALSE: whether to keep reads that do not classify below phylum, default = FALSE

keep.human

TRUE or FALSE: whether to keep reads that are classified as human, default = FALSE

Value

metagenomeseq object for downstream analysis with WIMP data

See also

metagenomeSeq

Examples

if (FALSE) {
wimp_raw_to_metagenomeseq(path.to.wimp.files = path/to/wimpfiles,
metadata = metadata, keep.unclassified = FALSE, keep.human = FALSE)
}