makeWindows.RdSplit 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.
query = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 11, 21), end = c(10, 20, 30))) makeWindows(query, w = 2)#> GRanges object with 15 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-2 * | 1 1 #> [2] chr1 3-4 * | 1 2 #> [3] chr1 5-6 * | 1 3 #> [4] chr1 7-8 * | 1 4 #> [5] chr1 9-10 * | 1 5 #> ... ... ... ... . ... ... #> [11] chr1 21-22 * | 3 1 #> [12] chr1 23-24 * | 3 2 #> [13] chr1 25-26 * | 3 3 #> [14] chr1 27-28 * | 3 4 #> [15] chr1 29-30 * | 3 5 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 0.5)#> GRanges object with 6 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-5 * | 1 1 #> [2] chr1 6-10 * | 1 2 #> [3] chr1 11-15 * | 2 1 #> [4] chr1 16-20 * | 2 2 #> [5] chr1 21-25 * | 3 1 #> [6] chr1 26-30 * | 3 2 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 3)#> GRanges object with 9 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-3 * | 1 1 #> [2] chr1 4-6 * | 1 2 #> [3] chr1 7-9 * | 1 3 #> [4] chr1 11-13 * | 2 1 #> [5] chr1 14-16 * | 2 2 #> [6] chr1 17-19 * | 2 3 #> [7] chr1 21-23 * | 3 1 #> [8] chr1 24-26 * | 3 2 #> [9] chr1 27-29 * | 3 3 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 3, direction = "reverse")#> GRanges object with 9 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 2-4 * | 1 1 #> [2] chr1 5-7 * | 1 2 #> [3] chr1 8-10 * | 1 3 #> [4] chr1 12-14 * | 2 1 #> [5] chr1 15-17 * | 2 2 #> [6] chr1 18-20 * | 2 3 #> [7] chr1 22-24 * | 3 1 #> [8] chr1 25-27 * | 3 2 #> [9] chr1 28-30 * | 3 3 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 3, short.keep = TRUE)#> GRanges object with 12 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-3 * | 1 1 #> [2] chr1 4-6 * | 1 2 #> [3] chr1 7-9 * | 1 3 #> [4] chr1 10 * | 1 4 #> [5] chr1 11-13 * | 2 1 #> ... ... ... ... . ... ... #> [8] chr1 20 * | 2 4 #> [9] chr1 21-23 * | 3 1 #> [10] chr1 24-26 * | 3 2 #> [11] chr1 27-29 * | 3 3 #> [12] chr1 30 * | 3 4 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 3, direction = "reverse", short.keep = TRUE)#> GRanges object with 12 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1 * | 1 1 #> [2] chr1 2-4 * | 1 2 #> [3] chr1 5-7 * | 1 3 #> [4] chr1 8-10 * | 1 4 #> [5] chr1 11 * | 2 1 #> ... ... ... ... . ... ... #> [8] chr1 18-20 * | 2 4 #> [9] chr1 21 * | 3 1 #> [10] chr1 22-24 * | 3 2 #> [11] chr1 25-27 * | 3 3 #> [12] chr1 28-30 * | 3 4 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 12)#> GRanges object with 0 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 12, short.keep = TRUE)#> GRanges object with 3 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-10 * | 1 1 #> [2] chr1 11-20 * | 2 1 #> [3] chr1 21-30 * | 3 1 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, k = 2)#> GRanges object with 6 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-5 * | 1 1 #> [2] chr1 6-10 * | 1 2 #> [3] chr1 11-15 * | 2 1 #> [4] chr1 16-20 * | 2 2 #> [5] chr1 21-25 * | 3 1 #> [6] chr1 26-30 * | 3 2 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, k = 3)#> GRanges object with 9 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-3 * | 1 1 #> [2] chr1 4-6 * | 1 2 #> [3] chr1 7-10 * | 1 3 #> [4] chr1 11-13 * | 2 1 #> [5] chr1 14-16 * | 2 2 #> [6] chr1 17-20 * | 2 3 #> [7] chr1 21-23 * | 3 1 #> [8] chr1 24-26 * | 3 2 #> [9] chr1 27-30 * | 3 3 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsquery = GRanges(seqnames = "chr1", ranges = IRanges(start = c(1, 11, 31), end = c(10, 30, 70))) makeWindows(query, w = 2)#> GRanges object with 35 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-2 * | 1 1 #> [2] chr1 3-4 * | 1 2 #> [3] chr1 5-6 * | 1 3 #> [4] chr1 7-8 * | 1 4 #> [5] chr1 9-10 * | 1 5 #> ... ... ... ... . ... ... #> [31] chr1 61-62 * | 3 16 #> [32] chr1 63-64 * | 3 17 #> [33] chr1 65-66 * | 3 18 #> [34] chr1 67-68 * | 3 19 #> [35] chr1 69-70 * | 3 20 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengthsmakeWindows(query, w = 0.2)#> GRanges object with 15 ranges and 2 metadata columns: #> seqnames ranges strand | .i_query .i_window #> <Rle> <IRanges> <Rle> | <integer> <integer> #> [1] chr1 1-2 * | 1 1 #> [2] chr1 3-4 * | 1 2 #> [3] chr1 5-6 * | 1 3 #> [4] chr1 7-8 * | 1 4 #> [5] chr1 9-10 * | 1 5 #> ... ... ... ... . ... ... #> [11] chr1 31-38 * | 3 1 #> [12] chr1 39-46 * | 3 2 #> [13] chr1 47-54 * | 3 3 #> [14] chr1 55-62 * | 3 4 #> [15] chr1 63-70 * | 3 5 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths