create_sample_sheet: Creates a sample sheet file names in the provided folder

Description Usage Arguments Examples

Description

This function would check for files ending in fastq.gz, fq.gz, fastq, fq.

Usage

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create_sample_sheet(path, project, subproject, runid, format,
  fix.names = FALSE, fix.names.char = "-", out_sep = c("\t", ","),
  include.undetermined = FALSE, pattern = "fastq.gz|fq.gz|fastq|fq",
  outfile)

Arguments

path

path to the fastq files

project

name of the project. optional

subproject

name of the subproject optional

runid

name of the flowcell this data is from optional

format

the format for names of fastq files, we have defaults for CASAVA and miSeq

fix.names

change the sample names such that they are acceptable as column names for R

pattern

extensions this function will look for optional

outfile

name of the output csv files optional

Examples

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## Not run: 
create_sample_mat(levelipath)

## End(Not run)

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.