Hi Is it possible to filter ranges by imposing condition on name field. I am using the IRanges vignette example below: Require(IRanges) ir1 <- IRanges(start = 1:10, width = 10:1) ir2 <- IRanges(start = 1:10, end = 11) ir3 <- IRanges(end = 11, width = 10:1) identical(ir1, ir2) & identical(ir2, ir3) ir <- IRanges(c(1, 8, 14, 15, 19, 34, 40), width = c(12, 6, 6, 15, 6, 2, 7)) values <- rnorm(length(ir)) rd <- RangedData(ir, name = letters[seq_len(length(ir))], values) rd 1> rd RangedData with 7 rows and 2 value columns across 1 space space ranges | name values <character> <iranges> | <character> <numeric> 1 1 [ 1, 12] | a -0.8204717 2 1 [ 8, 13] | b -0.2419617 3 1 [14, 19] | c -0.7747140 4 1 [15, 29] | d -0.1103875 5 1 [19, 24] | e -0.2945884 6 1 [34, 35] | f 1.8082479 7 1 [40, 46] | g -0.1854162 I have another list *toFind*: toFind = c ('a', 'c', 'd', 'f') Is it possible to find the correponding ranges? The output in this case would be 1> output RangedData with 4 rows and 2 value columns across 1 space space ranges | name values <character> <iranges> | <character> <numeric> 1 1 [ 1, 12] | a -0.8204717 2 1 [14, 19] | c -0.7747140 3 1 [15, 29] | d -0.1103875 4 1 [34, 35] | f 1.8082479 Thanks a lot. Fahim -- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 [[alternative HTML version deleted]]

On 03/12/2011 06:41 AM, Fahim Mohammad wrote: > Hi > Is it possible to filter ranges by imposing condition on name field. I am > using the IRanges vignette example below: > > Require(IRanges) > ir1 <- IRanges(start = 1:10, width = 10:1) > ir2 <- IRanges(start = 1:10, end = 11) > ir3 <- IRanges(end = 11, width = 10:1) > identical(ir1, ir2) & identical(ir2, ir3) > ir <- IRanges(c(1, 8, 14, 15, 19, 34, 40), > width = c(12, 6, 6, 15, 6, 2, 7)) > > values <- rnorm(length(ir)) > rd <- RangedData(ir, name = letters[seq_len(length(ir))], values) > rd > 1> rd > RangedData with 7 rows and 2 value columns across 1 space > space ranges | name values > <character> <iranges> | <character> <numeric> > 1 1 [ 1, 12] | a -0.8204717 > 2 1 [ 8, 13] | b -0.2419617 > 3 1 [14, 19] | c -0.7747140 > 4 1 [15, 29] | d -0.1103875 > 5 1 [19, 24] | e -0.2945884 > 6 1 [34, 35] | f 1.8082479 > 7 1 [40, 46] | g -0.1854162 > > > I have another list *toFind*: > > toFind = c ('a', 'c', 'd', 'f') > > Is it possible to find the correponding ranges? The output in this case > would be Hi Fahim -- access the 'name' field rd[["name"]] and use R's %in% to see which are in toFind; this is a logical vector that can be used to subset rd, as > rd[rd[["name"]] %in% toFind, ] RangedData with 4 rows and 2 value columns across 1 space space ranges | name values <character> <iranges> | <character> <numeric> 1 1 [ 1, 12] | a -0.02434458 2 1 [14, 19] | c 0.43727261 3 1 [15, 29] | d 0.92065069 4 1 [34, 35] | f 0.66271368 > > 1> output > RangedData with 4 rows and 2 value columns across 1 space > space ranges | name values > <character> <iranges> | <character> <numeric> > 1 1 [ 1, 12] | a -0.8204717 > 2 1 [14, 19] | c -0.7747140 > 3 1 [15, 29] | d -0.1103875 > 4 1 [34, 35] | f 1.8082479 > > > Thanks a lot. > Fahim > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793