Description Usage Arguments Details Value Author(s) Examples
Split Regions into Windows
1 2 | makeWindows(query, w = NULL, k = NULL, direction = c("normal", "reverse"),
short.keep = FALSE)
|
query |
A |
w |
Window size. A value larger than 1 means the number of base pairs and a value between 0 and 1 is the percent to the current region. |
k |
Number of partitions for each region. If it is set, all other arguments are ignored. |
direction |
Where to start the splitting? See 'Details' section. |
short.keep |
If the the region can not be split equally under the window size, the argument controls whether to keep the windows that are smaller than the window size. See 'Details' section. |
Following illustrates the meaning of direction
and short.keep
:
1 2 3 4 5 |
A GRanges-class
object with two additional columns attached:
.i_query
which contains the correspondance between small windows and original regions in query
.i_window
which contains the index of the small window on the current region.
Zuguang gu <z.gu@dkfz.de>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | query = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 11, 21), end = c(10, 20, 30)))
makeWindows(query, w = 2)
makeWindows(query, w = 0.5)
makeWindows(query, w = 3)
makeWindows(query, w = 3, direction = "reverse")
makeWindows(query, w = 3, short.keep = TRUE)
makeWindows(query, w = 3, direction = "reverse", short.keep = TRUE)
makeWindows(query, w = 12)
makeWindows(query, w = 12, short.keep = TRUE)
makeWindows(query, k = 2)
makeWindows(query, k = 3)
query = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 11, 31), end = c(10, 30, 70)))
makeWindows(query, w = 2)
makeWindows(query, w = 0.2)
|
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