callInteractions {UMI4Cats} | R Documentation

## Call significant interactions

### Description

Test a set of `query_regions` for significant interactions with the viewpoint.

### Usage

    callInteractions(
      umi4c,
      design = ~condition,
      query_regions,
      padj_method = "fdr",
      zscore_threshold = 2,
      padj_threshold = 0.1,
      alpha = 20,
      penalty = 0.1
    )

### Arguments

`umi4c` | UMI4C object as generated by `makeUMI4C` or the `UMI4C` constructor.
`design` | A `formula` or `matrix`. The formula expresses how the counts for each fragment end depend on the variables in `colData`. See `DESeqDataSet`.
`query_regions` | `GRanges` object or `data.frame` containing the coordinates of the genomic regions you want to use to perform the analysis in specific genomic intervals. Default: NULL.
`padj_method` | The method to use for adjusting p-values, see `p.adjust`. Default: fdr.
`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. `floor((max(number of fragments)) / alpha)` is passed to `create.bspline.basis` as nbasis argument. 4 is the minimum allowed value. Default: 20.
`penalty` | Amount of smoothing to be applied to the estimated functional parameter. Default: 0.1.

### Value

`GRangesList` where each element is a UMI4C sample with the queried regions and their adjusted p-values and Z-scores.

### Examples

    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)

[Package UMI4Cats version 1.4.0 Index]