Match sample names from sam_data and fastq files
Source:R/targets_misc.R
sam_data_matching_names.Rd
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.