Creates a new track from smoothed values of track expression

Creates a new track from smoothed values of track expression.

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

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

Value

None.

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.

See also

gtrack.create, gtrack.2d.create, gtrack.create_sparse, gtrack.modify, gtrack.rm, gtrack.info, gdir.create

Examples

# \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))
#>    chrom start  end dense_track smoothed_track intervalID
#> 1   chr1     0   50   0.1777778     0.17079365          1
#> 2   chr1    50  100   0.1600000     0.17034188          1
#> 3   chr1   100  150   0.1800000     0.17037037          1
#> 4   chr1   150  200   0.1600000     0.16949494          1
#> 5   chr1   200  250   0.1600000     0.16615874          1
#> 6   chr1   250  300   0.2000000     0.16049382          1
#> 7   chr1   300  350   0.1600000     0.14888889          1
#> 8   chr1   350  400   0.1600000     0.13444445          1
#> 9   chr1   400  450   0.1600000     0.11555555          1
#> 10  chr1   450  500   0.0600000     0.09277777          1
#> 11  chr1   500  550   0.0600000     0.07111111          1
#> 12  chr1   550  600   0.0200000     0.05055555          1
#> 13  chr1   600  650   0.0400000     0.03500000          1
#> 14  chr1   650  700   0.0000000     0.02277778          1
#> 15  chr1   700  750   0.0000000     0.01611111          1
#> 16  chr1   750  800   0.0000000     0.01666667          1
#> 17  chr1   800  850   0.0000000     0.01888889          1
#> 18  chr1   850  900   0.0200000     0.02333333          1
#> 19  chr1   900  950   0.0400000     0.02722222          1
#> 20  chr1   950 1000   0.0400000     0.03000000          1
gtrack.rm("smoothed_track", force = TRUE)