Description Usage Arguments Details Value Author(s)
Try to detect repeats that have gotten longer than the typical inner mate distance
1 2 3 | FacingVersusFlanking(facing_file_list,
flanking_file_list, pheno_table, min_total_counts = 50,
output_dir = "~", prefix)
|
facing_file_list |
list of all .facing sample files |
flanking_file_list |
list of all .flanking sample files |
pheno_table |
ExpressionPlot type pheno table |
min_total_counts |
miniumum total number of read pairs associated with a given repeat across all samples |
output_file |
path to and name of file to output results to. |
Uses the edgeR package to try and detect differential read class frequencies (facing versus flanking) between tumor and normal samples.
TSV file
Adam Struck - Intern
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