calcApa | R Documentation |
Extract BEDPE interactions from a Hi-C matrix
calcApa( bedpe, hic, norm = "NONE", res = 10000, buffer = 5, filter = FALSE, matrix = "observed" )
bedpe |
data.frame or data.table in BEDPE format. |
hic |
string path to .hic file. |
norm |
string hic normalization <NONE/VC/VC_SQRT/KR>. |
res |
integer resolution of bedpe bins. |
buffer |
integer number of res-length bins from the center pixel. |
filter |
TRUE or FALSE (default). If TRUE, |
matrix |
Type of matrix to output. Can be one of observed/oe/expected. observed is observed counts, oe is observed/expected counts, expected is expected counts. |
Returts a list APA matricies that can be compiled and plotted.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.