makeWindows: Split Regions into Windows

In EnrichedHeatmap: Making Enriched Heatmaps

Description

Split Regions into Windows

Usage

makeWindows(query, w = NULL, k = NULL, direction = c("normal", "reverse"),
    short.keep = FALSE)

Arguments

query	A GRanges-class object.
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.

Details

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  

Value

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.

Author(s)

Zuguang gu <[e-mail]>

Examples

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)

EnrichedHeatmap documentation built on Nov. 8, 2020, 8:20 p.m.