Import the metadata and check it is correct
sanity_check(sample.info, reference = NULL, species = c("human", "mouse"), output.dir, threads = NULL)
| sample.info | character string giving the path to a tab-delimited text file with at least the columns <condition> (treatment condition), <sample> (sample name), and <file1> (absolute or relative path to the fastq files). If fastq files and PE reads, then a column <file2> should also be present. If a batch effect is to be included in the design, then this should be identified under the column <batch>. If IP controls are used then these should be specified in columns <input1> (and <input2> if paired reads); this is not necessary for ATAC-seq. |
|---|---|
| reference | character vector specifying the conditions in order. For example,
c("A", "B", "C", "D") would mean "A" is the reference condition to which "B", "C"
and "D" are compared; in addition, "C" and "D" will be compared to "B", and "D"
will be compared to "C". If |
| species | character string specifying the name of the species. Only
|
| output.dir | character string specifying the directory to which results will be saved. If the directory does not exist, it will be created. |
| threads | an integer value indicating the number of parallel threads to be used by FastQC. [DEFAULT = maximum number of available threads - 1]. |
A data.frame