as.normalizedMatrix: Convert a Normal Matrix to a normalizedMatrix Object
In jokergoo/EnrichedHeatmap: Making Enriched Heatmaps

as.normalizedMatrix

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.