sam_data_matching_names: Match sample names from sam_data and fastq files

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Match sample names from sam_data and fastq files

Description

Useful for targets bioinformatic pipeline.

Usage

sam_data_matching_names(
  path_sam_data,
  sample_col_name,
  path_raw_seq,
  pattern_remove_sam_data = NULL,
  pattern_remove_fastq_files = NULL,
  verbose = TRUE,
  remove_undocumented_fastq_files = FALSE,
  prefix = NULL,
  ...
)

Arguments

path_sam_data	(Required) Path to sample data file.
sample_col_name	(Required) The name of the column defining sample names in the sample data file.
path_raw_seq	(Required) Path to the folder containing fastq files
pattern_remove_sam_data	If not null, describe the pattern that will be deleted from sam_data samples names.
pattern_remove_fastq_files	If not null, describe the pattern that will be deleted from fastq files names.
verbose	(logical, default TRUE) If TRUE, print some additional messages.
remove_undocumented_fastq_files	(logical, default FALSE) If set to TRUE fastq files not present in sam_data are removed from your folder. Keep a copy of those files somewhere before.
prefix	Add a prefix to new samples names (ex. prefix = "samp")
...	Other parameters passed on to utils::read.csv() function.

Value

A list of two objects :

• $sam_names_matching is a tibble of corresponding samples names

• $sam_data is a sample data files including only matching sample names

Author(s)

Adrien Taudière

adrientaudiere/MiscMetabar documentation built on Dec. 19, 2024, 3:16 a.m.