presegment | R Documentation |
pre-segmentation of the time-series into chunks that can be handled by segmenTier.
presegment(
ts,
avg = 1000,
minrd = 8,
favg = 100,
border = c("expand", "trim"),
minds = 250,
rmlen = 250,
minsg = 5000,
chrS,
map2chrom = FALSE,
seg.path,
plot.borders = FALSE,
fig.path,
fig.type = "png",
verb = 1
)
ts |
the time-series of readcounts for the complete chromosome,
rows are chromosomal positions and columns are time-points; reverse
strand rows at the bottom of the matrix. Option |
avg |
the broad moving average of read-count presence (number of time-points with >0 reads) for a first broad segmentation |
minrd |
the minimal number of time-points with reads in the broad moving average used as cutoff between segments |
favg |
as |
border |
string indicating whether to "expand" or "trim" borders,
using the finer moving average in |
minds |
minimum distance between two segments (will be fused if distance is smaller) |
rmlen |
minimum segment length for removal (shorter segments will be dropped) |
minsg |
minimum segment length for fusion with (shorter) neighbor |
chrS |
a chromosome index, indicating at wich positions chromosomes start; this is required for handling chromosome ends and forward and reverse strand values, but can be omitted. |
map2chrom |
if true, argument |
seg.path |
a directory path where individual segments' data will
be written to as tab-delimited .csv files; no files will be written if
|
plot.borders |
logical indicating whether plots of the scanned
borders should be generate (in directory at |
fig.path |
a directory path for plots of the segment end scanning;
no figures will be plotted if |
fig.type |
image type, "png" or "pdf" |
verb |
integer level of verbosity, 0: no messages, 1: show messages |
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