makeWindows {EnrichedHeatmap} | R Documentation |
Split regions into windows
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
:
-->-->-->- one region, split by 3bp window (">" represents the direction of the sequence) aaabbbccc direction = "normal", short.keep = FALSE aaabbbcccd direction = "normal", short.keep = TRUE aaabbbccc direction = "reverse", short.keep = FALSE abbbcccddd direction = "reverse", short.keep = TRUE
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>
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)