Description Usage Arguments Value
Import the metadata and check it is correct
1 2 | 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 or salmon quant.sf 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>. |
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
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