centerAtMax {seqsetvis} | R Documentation

## centers profile of x and y. default is to center by region but across all samples.

### Description

`centerAtMax` locates the coordinate x of the maximum in y and shifts x such that it is zero at max y.

### Usage

    centerAtMax(dt, x_ = "x", y_ = "y", by_ = "id", view_size = NULL,
      trim_to_valid = TRUE, check_by_dupes = TRUE, x_precision = 3,
      replace_x = TRUE)

### Arguments

`dt` | data.table
`x_` | the variable name of the x-values. default is 'x'
`y_` | the variable name of the y-values default is 'y'
`by_` | optionally, any variables that provide grouping to the data. default is none. see details.
`view_size` | the size in `x_` to consider for finding the max of `y_`. if length(view_size) == 1, range will be c(-view_size, view_size). if length(view_size) > 1, range will be range(view_size). default value of NULL uses complete range of x.
`trim_to_valid` | valid `x_` values are those with a set `y_` value in all `by_` combinations
`check_by_dupes` | default assumption is that there should be on set of x_ for a by_ instance. if this is not the case and you want to disable warnings about set this to FALSE.
`x_precision` | numerical precision of x, default is 3.
`replace_x` | logical, default TRUE. if TRUE x_ will be replaced with position relative to summit. if FALSE x_ will be preserved and x_summitPosition added.

### Details

character. by_ controls at the level of the data centering is applied. If by_ is "" or NULL, a single max position will be determined for the entire dataset. If by is "id" (the default) then each region will be centered individually across all samples.

### Value

data.table with x (or xnew if replace_x is FALSE) shifted such that x = 0 matches the maximum y-value define by by_ grouping

### Examples

    centerAtMax(CTCF_in_10a_profiles_gr, y_ = 'y', by_ = 'id',
      check_by_dupes = FALSE)
    #it's a bit clearer what's happening with trimming disabled
    #but results are less useful for heatmaps etc.
    centerAtMax(CTCF_in_10a_profiles_gr, y_ = 'y', by_ = 'id',
      check_by_dupes = FALSE, trim_to_valid = FALSE)
    #specify view_size to limit range of x values considered, prevents
    #excessive data trimming.
    centerAtMax(CTCF_in_10a_profiles_gr, y_ = 'y', view_size = 100, by_ = 'id',
    check_by_dupes = FALSE)

[Package seqsetvis version 1.4.1 Index]