maxGapminRun {biomvRCNS} | R Documentation |
A custom Max-gap-min-run implementation using physical position for gap and run length calculation.
maxGapminRun(x, xPos = NULL, xRange = NULL, cutoff = NULL, q = 0.9, high=TRUE, minrun = 5, maxgap = 2, splitLen = Inf, na.rm=TRUE)
x |
a numeric vector for the input signal |
xPos |
a numeric vector, same length as x, carrying positional information for each element of x |
xRange |
an |
cutoff |
numeric value used as cut-off, optional if |
q |
numeric value used to derive cut-off of x, as the |
high |
TRUE if the |
minrun |
minimum run length for the resulting segments |
maxgap |
maximum genomic distance below which two adjacent qualified tiles can be joined |
splitLen |
numeric value, maximum length of segments, split if too long |
na.rm |
|
A custom Max-gap-min-run implementation using physical position for gap and run length calculation.
a list of segment starts and ends indices
IS |
the start index for each segment |
IE |
the end index for each segment |
CUTOFF |
the cutoff value used in the run |
MG |
the parameter value for |
MR |
the parameter value for |
SPL |
the parameter value for |
Yang Du
biomvRhsmm
biomvRseg
biomvRmgmr
x<-rpois(50, 10) xpos<-rnorm(50, 300, 100) xpos<-xpos[order(xpos)] maxGapminRun(x, xpos, cutoff=9.5, maxgap=30, minrun=100)