as.normalizedMatrix {EnrichedHeatmap} | R Documentation

## Convert a Normal Matrix to a normalizedMatrix Object

### Description

Convert a Normal Matrix to a normalizedMatrix Object

### Usage

    as.normalizedMatrix(mat, k_upstream = 0, k_downstream = 0, k_target = 0,
        extend, signal_name = "signals", target_name = "targets",
        background = NA, smooth = FALSE, smooth_fun = default_smooth_fun,
        keep = c(0, 1), trim = NULL)

### Arguments

`mat` | A matrix generated by other software.
`k_upstream` | Number of windows in the upstream.
`k_downstream` | Number of windows in the downstream.
`k_target` | Number of windows in the target.
`extend` | Extension to the target. The length should be 1 (if one of `k_upstream` or `k_downstream` is zero). or 2 (if both of `k_upstream` and `k_downstream` are non-zero).
`signal_name` | The name of signal regions. It is only used for printing the object.
`target_name` | The name of the target names. It is only used for printing the object.
`background` | The background value in the matrix.
`smooth` | Whether apply smoothing on rows in the matrix.
`smooth_fun` | The smoothing function that is applied to each row in the matrix. This self-defined function accepts a numeric vector (may contain `NA` values) and returns a vector with same length. If the smoothing is failed, the function should call `stop` to throw errors so that `normalizeToMatrix` can catch how many rows are failed in smoothing. See the default `default_smooth_fun` for example.
`keep` | Percentiles in the normalized matrix to keep. The value is a vector of two percent values. Values less than the first percentile is replaces with the first pencentile and values larger than the second percentile is replaced with the second percentile.
`trim` | Deprecated, please use `keep` instead.

### Details

If users use the matrix from other software, they can use this function to convert it to the `normalizedMatrix` object and visualize it afterwards.

### Value

A `normalizedMatrix` object.

### Author(s)

z.gu@dkfz.de

### Examples

    # There is no example
    NULL

[Package EnrichedHeatmap version 1.16.0 Index]