wimp_raw_to_metagenomeseq: Raw WIMP files plus metadata to metagenomeseq object

In epi2me2r: Process Nanopore EPI2ME Output for Use in R

Raw WIMP files plus metadata to metagenomeseq object

Description

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

## Not run: 
wimp_raw_to_metagenomeseq(path.to.wimp.files = path/to/wimpfiles,
metadata = metadata, keep.unclassified = FALSE, keep.human = FALSE)

## End(Not run)

epi2me2r documentation built on June 3, 2022, 9:07 a.m.