segReadsGeneric {PICS} | R Documentation |
Perform genome segmentation depending
Description
Perform genome segmentation depending
Usage
segReadsGeneric(
data,
dataC = NULL,
map = NULL,
minReads = 2,
minReadsInRegion = 3,
jitter = FALSE,
maxLregion = 0,
minLregion = 100,
step = 20,
width = 250,
package = "PICS"
)
Arguments
data |
A GRanges object containing the IP reads. See details for
more information on how to set up the data.
|
dataC |
A GRanges object containing the control reads. Set to NULL
by default, i.e. no control.
|
map |
A GRanges object containing the mappability profiles. Set
to NULL by default, i.e. no profiles.
|
minReads |
A numeric . The minimum number of F/R reads to be
present in the sliding window.
|
minReadsInRegion |
A numeric . The minimum number of F/R reads
to be present in the region.
|
jitter |
A logical value stating whether some noise should be
added to the read locations. This is recommended if the read positions have
lots of duplicates.
|
maxLregion |
A numeric . The maximum length.
|
minLregion |
A numeric . The minimum length.
|
step |
A numeric . The increment of the sliding window.
|
width |
A numeric . The width of the region.
|
package |
A character . "PICS" or "PING"
|
[Package
PICS version 2.36.0
Index]