Compress genome coordinates of a matrix of polygons
compressPolygonM(polyM, ref2c, minRatio = 5, verbose = FALSE, ...)
polyM | data.frame including |
---|---|
ref2c | list output from |
minRatio | the minimum ratio of coordinate compression required before polygon resolution is downsampled. |
verbose | logical indicating whether to print verbose output. |
... | additional arguments are ignored. |
data.frame with the same colnames, with reduced rows
for polygons where the coordinate compression defined in
ref2c
is above minRatio
ratio. The compressed coverage roughly
represents the max coverage value for each point.
This function takes a two-column numeric matrix of polygons
where the x coordinate is the genomic position, and y coordinate
is the coverage. It uses ref2compressed$transform
to convert
coordinates to compressed coordinates, as output from
make_ref2compressed()
.
For regions that have been compresssed, it then compresses the y-coordinate information to roughly one y value per integer in compressed coordinate space, using the runmax across the window of coverages compressed to this value.
Other jam spatial functions:
bgaPlotly3d()
,
dfWide2segments()
,
simplifyXY()
,
spline3d()