getSampleName: Get Sample Name from Fastq Filename (DEPRECATED)

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

Get Sample Name from Fastq Filename (DEPRECATED)

Description

Deprecated in favor of code that reads dnaSampleID from sequence metadata.

Usage

getSampleName(
  fn,
  post_samplename_pattern1 = "_R1.*\\.fastq",
  post_samplename_pattern2 = "_R2.*\\.fastq"
)

Arguments

fn	Fastq filename(s).
post_samplename_pattern1, post_samplename_pattern2	Default "_R1.\.fastq" and "_R2.\.fastq". Regular expressions denoting the ends of the R1 and R2 filenames, respectively, which will be trimmed away, leaving identical names between corresponding R1 and R2 files.

Details

Extracts the sample names from fastq filenames, given regular expressions denoting the different endings of R1 and R2 filenames.

Value

Character vector; sample names of the input fastq filenames.

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