getPairedFastqFiles: Get Paired Fastq Files

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

Get Paired Fastq Files

Description

Given a vector of fastq file names and corresponding metadata, outputs a list containing matching R1 and R2 files in the same order. Useful for providing files to functions that utilize filterAndTrim, such as trimPrimer16S and runDadaITS.

Usage

getPairedFastqFiles(fn, meta, value = TRUE, verbose = TRUE)

Arguments

fn	Full name(s) of fastq file(s). Tolerant to filenames with appended run ID prefix (e.g. "runB69RN_...") and agnostic to .gz compression.
meta	Metadata downloaded using downloadSequenceMetadata that corresponds to the fastq files.
value	(Optional) Default TRUE; returns file names. If FALSE, returns indices.
verbose	(Optional) Default TRUE. Whether to print warning messages when metadata does not contain records corresponding to all provided fastq files.

Details

See related function: removeUnpairedFastqFiles.

Value

List of length 2; first element contains matched R1 (forward) file names, and second element contains corresponding R2 (reverse) file names.

Examples

## Not run: 
#' matched_fn <- getPairedFastqFiles(c("sample1_R1.fastq", "sample3_R1.fastq", "sample1_R2.fastq", "sample2_R2.fastq", "sample3_R2.fastq"), meta)
fnFs <- matched_fn[[1]] # "sample1_R1.fastq" "sample3_R1.fastq"
fnRs <- matched_fn[[2]] # "sample1_R2.fastq" "sample3_R2.fastq"

## End(Not run)

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