gtrack.smooth: Creates a new track from smoothed values of track expression

Description

Creates a new track from smoothed values of track expression.

Usage

gtrack.smooth(
  track = NULL,
  description = NULL,
  expr = NULL,
  winsize = NULL,
  weight_thr = 0,
  smooth_nans = FALSE,
  alg = "LINEAR_RAMP",
  iterator = NULL
)

Value

None.

Arguments

track: track name
description: a character string description
expr: track expression
winsize: size of smoothing window
weight_thr: smoothing weight threshold
smooth_nans: if 'FALSE' track value is always set to 'NaN' if central window value is 'NaN', otherwise it is calculated from the rest of non 'NaN' values
alg: smoothing algorithm - "MEAN" or "LINEAR_RAMP"
iterator: track expression iterator of 'Fixed bin' type

Details

This function creates a new 'Dense' track named 'track'. The values of the track are results of smoothing the values of 'expr'.

Each track value at coordinate 'C' is determined by smoothing non 'NaN' values of 'expr' over the window around 'C'. The window size is controlled by 'winsize' and is given in coordinate units (not in number of bins), defining the total regions to be considered when smoothing (on both sides of the central point). Two different algorithms can be used for smoothing:

"MEAN" - an arithmetic average.

"LINEAR_RAMP" - a weighted arithmetic average, where the weights linearly decrease as the distance from the center of the window increases.

'weight_thr' determines the function behavior when some of the values in the window are missing or 'NaN' (missing values may occur at the edges of each chromosome when the window covers an area beyond chromosome boundaries). 'weight_thr' sets the weight sum threshold below which smoothing algorithm returns 'NaN' rather than a smoothing value based on non 'NaN' values in the window.

'smooth_nans' controls what would be the smoothed value if the central value in the window is 'NaN'. If 'smooth_nans' is 'FALSE' then the smoothed value is set to 'NaN' regardless of 'weight_thr' parameter. Otherwise it is calculated normally.

'description' is added as a track attribute.

Iterator policy must be of "fixed bin" type.

Examples

Run this code

# \dontshow{
options(gmax.processes = 2)
# }

gdb.init_examples()
gtrack.smooth("smoothed_track", "Test track", "dense_track", 500)
gextract("dense_track", "smoothed_track", gintervals(1, 0, 1000))
gtrack.rm("smoothed_track", force = TRUE)