search for: triplet

I have a list (length 750), each element containing a vector of unique strings (unique gene ids), with length up to ~40 (median 15). I want to compile a matrix of all possible triplets and their frequency within gene elements. Using combn and a lot of looping, I am accomplishing this but it is VERY slow. I've tried to figure out a way to vectorize this, using "match" and "%in%", but can't get my mind around it. Below is my code. sig.tf.pairs is t...

...match what everyone else does. This will break existing key files, though, which is unfortunate. - todd diff --git a/src/utils.c b/src/utils.c index fadfd05..43d4840 100644 --- a/src/utils.c +++ b/src/utils.c @@ -75,14 +75,14 @@ int b64decode(const char *src, void *dst, int length) { uint32_t triplet = 0; unsigned char *udst = (unsigned char *)dst; - for(i = 0; i < length && src[i]; i++) { - triplet |= base64_decode[src[i] & 0xff] << (6 * (i & 3)); + for(i = 0; i < length && src[i] && src[i] != '='; i++) { + triplet = (triplet << 6...

I'm attempting to create a sequence for an experiment and am hoping I can use R to create it. It has several constraints: (1) It is made up of two sequences (red and green) that have 4 different repeating triplets (e.g. T1=ABC T2=DEF T3=GHI JKL) (2) Each sequence has the following constraints: (a) there cannot be repeating triplets (e.g. T1 T1), (b) there cannot be repeating triplet pairs (e.g. T1 T2 T1 T2) (3) Triplets occur with the following frequency: T1=20, T2=23, T3=26, T4=36 (same for red and green s...

...at3d[,,2] <- round(rescale(mat3d[,,2],oldmin=mini[2],oldmax=maxi[2],newmax=ngris-1)) mat3d[,,3] <- round(rescale(mat3d[,,3],oldmin=mini[3],oldmax=maxi[2],newmax=ngris-1)) } #stretching #2. Generates z vectors from a (m,n,3) array. i1 <- rep(1:m,rep(n,m)) i2 <- rep(1:n,m) tripletes <-cbind(mat3d[cbind(i1,i2,1)],mat3d[cbind(i1,i2,2)],mat3d[cbind(i1,i2,3)]) #Note: triplets are ordered by rows #3. Generates RGB colors: tripletes <- tripletes/ngris cols <- rgb(tripletes[,1],tripletes[,2],tripletes[,3]) #Formats vector of color codes as (m,n) matrix: dim(cols...

First, happy holidays, everyone! Thanks to the R team for bringing out 1.4 before the new year. I have 10000 integer triplets stored in A[1:10000, 1:3]. I would like to find the unique triplets among the 10000 ones with possible duplications. What is the easiest way for this. I know the function unique(), which apply to a vector, not the 10000*3 array in my problem. Thanks in advance. Jason ===== Jason G. Liao, Ph.D....

I think that this is an easy one... I have a matrix where each row is an (x,y,z) triplet. Given a potential (xnew,ynew,znew) triplet I want to know if the matrix already contains a row with the new values (the space already has that point). I can do it using a for loop, but I would like to know if there is anyway in which I can do it without the for loop. I do it now like this (th...

...oongson/src/llvm-2.7/include -g0 -finhibit-size-directive -fno-inline-functions -fno-exceptions -fno-zero-initialized-in-bss -fno-toplevel-reorder -Dinhibit_libc \ > -c ../../../src/llvm-gcc-4.2-2.7.source/gcc/crtstuff.c -DCRT_BEGIN \ > -o crtbegin.o > Did not get a target machine! Triplet is mips64el-unknown-linux-gnu > make[1]: *** [crtbegin.o] Error 1 > make[1]: Leaving directory `/home/ext3/loongson/build/llvm-gcc/gcc' > make: *** [all-gcc] Error 2 > > > -- > Wei Wu > wuwei08 at iscas.ac.cn > > _______________________________________________...

...e -I/home/ext3/loongson/src/llvm-2.7/include -g0 -finhibit-size-directive -fno-inline-functions -fno-exceptions -fno-zero-initialized-in-bss -fno-toplevel-reorder -Dinhibit_libc \ -c ../../../src/llvm-gcc-4.2-2.7.source/gcc/crtstuff.c -DCRT_BEGIN \ -o crtbegin.o *Did not get a target machine! Triplet is mips64el-unknown-linux-gnu* make[1]: *** [crtbegin.o] Error 1 make[1]: Leaving directory `/home/ext3/loongson/build/llvm-gcc/gcc' make: *** [all-gcc] Error 2 -- Wei Wu wuwei08 at iscas.ac.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.l...

...wrote: >> Sounds fine to me. I just wanted some convenient and consistent naming. >> I think it conflicts a bit with the triples (-win32 currently means >> msvc I think), > Right. But this is again a historical (and LLVM-specific) artifact, > because I doubt anyone uses such triplet outside to mean msvc > compatibility. > Fair enough. Mostly most of the triples that exist aren't very useful for strict msvc compatibility since it wasn't a mode that gcc embraced :) >> but that'll probably be ok ultimately - internal function names are easy to >> r...

...t root from any IP b) accept RSA authentication for root from a couple IPs/Netmasks c) accept password authentication for all but root from a dozen Netmasks d) accept password authentication for root from 3 local netmasks only ie. make authentication depend on the USER,METHOD,CLIENT-IP triplet... Cheers, MaZe.

...9; package, I have not been able to figure out how the plot() method converts colorspace coordinates to RGB values for display on the screen. I am convert between colorspaces with the various as() methods... but cannot seem to find a way to extract RGB (i.e. for displaying on a computer screen) triplets from color space coordinates. Here is a sample of the data that I am working with: H V C x y Y 2.5Y 0.2 2 1.43 0.97 0.237 2.5Y 0.4 2 0.729 0.588 0.467 2.5Y 0.6 2 0.563 0.491 0.699 2.5Y 0.6...

...ds fine to me. I just wanted some convenient and consistent naming. > >> I think it conflicts a bit with the triples (-win32 currently means > >> msvc I think), > > Right. But this is again a historical (and LLVM-specific) artifact, > > because I doubt anyone uses such triplet outside to mean msvc > > compatibility. > > > > Fair enough. Mostly most of the triples that exist aren't very useful for > strict > msvc compatibility since it wasn't a mode that gcc embraced :) Yeah, right now we have the -cxx-abi microsoft flag. We could put ms...

...pasa si estas categorías son la presencia de objetos de la casa para clasificar la casa? Quiero decir, techo, pieza es casa común. Otro es techo, pieza, pileta es casa grande. Pero otro usuario solo ingresa pieza y pileta (supone que hay techo) y también es casa grande. En el primer caso tengo dos tripletes (0,0,0 techo y 0,0,1 pieza) En el segundo caso tres tripletes porque hay tres objetos. En el tercero solo tiene dos tripletes, suponiendo la existencia de techo en una casa. En un ejemplo como este donde hay tres objetos de casa, podría entrenarla sin problemas porque hay unas 9 posibilidades de...

In the Matrix package v. 0.995-11 I see that the dgTMatrix Class for compressed, sparse, triplet-form matrices handles Identically indexed data instances by summing their values, e.g., library(Matrix) (Mt <- new("dgTMatrix", i = as.integer(c(0,0,1,1,4)), j = as.integer(c(0,1,2,2,4)), x = as.double(1:5), Dim = as.integer(c(5,5)))) ## 5 x 5 sparse Matrix of class &quo...

In the Matrix package v. 0.995-11 I see that the dgTMatrix Class for compressed, sparse, triplet-form matrices handles Identically indexed data instances by summing their values, e.g., library(Matrix) (Mt <- new("dgTMatrix", i = as.integer(c(0,0,1,1,4)), j = as.integer(c(0,1,2,2,4)), x = as.double(1:5), Dim = as.integer(c(5,5)))) ## 5 x 5 sparse Matrix of class &quo...

Hey all, I'm currently working through the problems at Project Euler -- this question came up while working on Problem 9 (http://projecteuler.net/problem=9): "A Pythagorean triplet is a set of three natural numbers, a < b < c, for which, a^2 + b^2 = c^2. For example, 3^2 + 4^2 = 9 + 16 = 25 = 5^2. There exists exactly one Pythagorean triplet for which a + b + c = 1000. Find the product abc." Not too hard: n=1000 for(i in 1:floor(n/3)) for(j in (i+1):floor(n/2-i...

...mentation) This would permit some advanced compilers using LLVM to return two or three pointers in registers, perhaps even (for hypothetically very clever compilers) in C or C++ return struct of 3 words in registers, not thru the stack, or some ML implementations returning a couple like (x,y) or triplet like (x,y,z) thru registers (without boxing the couple or triplet) Even having at most 2 results, ie the primary result and an optional secondary one could be very useful (eg returning both the sine and cosine of a float, or the remainder and the quotient of two non-zero integers). And the curre...

Hi, Can anybody tell me what the message below means and how to overcome it. Thanks, Neil Warning message: X matrix deemed to be singular; variable 2 in: coxph(Surv(age_at_death, death) ~ project$pluralgp + project$yrborn + ......... >

...tos de la casa > para clasificar la casa? > > Quiero decir, techo, pieza es casa común. > > Otro es techo, pieza, pileta es casa grande. > > Pero otro usuario solo ingresa pieza y pileta (supone que hay techo) y > también es casa grande. > > En el primer caso tengo dos tripletes (0,0,0 techo y 0,0,1 pieza) > > En el segundo caso tres tripletes porque hay tres objetos. > > En el tercero solo tiene dos tripletes, suponiendo la existencia de techo > en una casa. > > En un ejemplo como este donde hay tres objetos de casa, podría entrenarla > sin probl...

Hi, List, In checking the page fault problem when using pv-grub to start domU in opensuse12.3[1], found that the problem is caused by ''-fstack-protector'' flag which is introduced in rpm build: export EXTRA_CFLAGS_XEN_TOOLS="$RPM_OPT_FLAGS" export EXTRA_CFLAGS_QEMU_TRADITIONAL="$RPM_OPT_FLAGS" export EXTRA_CFLAGS_QEMU_XEN="$RPM_OPT_FLAGS" with