callInteractions {UMI4Cats} | R Documentation |
Test a set of query_regions
for significant interactions with the
viewpoint.
callInteractions( umi4c, design = ~condition, query_regions, padj_method = "fdr", zscore_threshold = 2, padj_threshold = 0.1, alpha = 20, penalty = 0.1 )
umi4c |
UMI4C object as generated by |
design |
A |
query_regions |
|
padj_method |
The method to use for adjusting p-values, see
|
zscore_threshold |
Numeric indicating the z-score threshold to use to define significant differential contacts. Default: 2. |
padj_threshold |
Numeric indicating the adjusted p-value threshold to use to define significant differential contacts. Default: 0.1. |
alpha |
Approximate number of fragments desired for every basis function
of the B-spline basis. |
penalty |
Amount of smoothing to be applied to the estimated functional parameter. Default: 0.1. |
GRangesList
where each element is a
UMI4C sample with the queried regions and their adjusted p-values and Z-scores.
data("ex_ciita_umi4c") umi <- ex_ciita_umi4c win_frags <- makeWindowFragments(umi, n_frags=8, sliding=1) gr <- callInteractions(umi, ~condition, win_frags, padj_threshold = 0.01, zscore_threshold=2) inter <- getSignInteractions(gr)