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...matrices A and B. And I want to measure how good each of this matrix is. So I intend to compare A and B with another "gold standard" matrix X. Meaning the more similar a matrix to X the better it is. What is the common way in R to measure matrix similarity (ie. A vs X, and B vs X) ? - Gundala Viswanath Jakarta - Indonesia

..., "AAG", "ATA", "ATT") > qr <- c("AAC", "ATT", "ATT") > which(repo%in%qr) [1] 3 6 Note that the query contain repeating elements, yet the output of which only returns unique. How can I make it returning [1] 3 6 6 instead? - Gundala Viswanath Jakarta - Indonesia

...x=c(rgamma(30,shape=.2,scale=14),rgamma(30,shape=12,scale=10),rgamma(30,shape=5,scale=6)) I want to plot the density curve of X, in a way that it shows a distinct 3 curves that represent each component. How can I do that? I tried this but doesn't work: lines(density(x)) Please advise. - Gundala Viswanath Jakarta - Indonesia

...3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 0 0 0 0 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 0 0 0 1 [3,] 0 0 0 0 0 0 0 0 0 2 I tried: > as.matrix(x) But failed. - Gundala Viswanath Jakarta - Indonesia

...0.05204063 [3,] 8.923553e-01 0.10764474 [4,] 9.295003e-01 0.07049966 [5,] 8.880434e-01 0.11195664 [6,] 9.197367e-01 0.08026327 [7,] 9.431232e-01 0.05687676 [8,] 9.460356e-01 0.05396442 [9,] 6.053829e-01 0.39461708 [10,] 9.515173e-01 0.04848268 Is there a simple way to do it in R? - Gundala Viswanath Jakarta - Indonesia

...ource array: > src [1] "bar" "pox" and the other one the complement. In the end we hope to get this two dataframes: > data_child1 V1 V2 bar 13.1 pox 8.21 and > data_child2_complement foo 13.1 qux 10.4 cho 20.33 Is there a compact way to do it in R? - Gundala Viswanath Jakarta - Indonesia

...21.4 32.4 49.7 51.3 58.3 58.9 11097 59.5 65.9 117.5 118.0 118.9 122.5 126.3 156.5 157.0 I want to get the label (first) column only: 11145 3545 8951 11097 Is there a quick way to achieve that? I tried this but fail: mylable <- dataf[,1] Please advice. - Gundala Viswanath Jakarta - Indonesia

Hi Dieter, Sorry my mistake. I wanted to convert them into Decimal (not Hexadecimal). Given this string, the desired answer follows: > ascii_str <- "ORQ>IK" 79 82 81 62 73 75 > ascii_str2 <- "FDC" 70 68 67 - Gundala Viswanath Jakarta - Indonesia On Mon, Dec 22, 2008 at 5:49 PM, Dieter Menne <dieter.menne at menne-biomed.de> wrote: > Gundala Viswanath <gundalav <at> gmail.com> writes: > >> For example I have the following ASCII strings: >> >> > ascii_str <- &q...

Hi, I have the following data that looks like this: > names(dat) [1] "(-2329,-2319]" "(-1399,-1389]" "(-669.4,-659.4]" How can I modify those names into just this? [1] -2329 -1399 -669.4 - Gundala Viswanath Jakarta - Indonesia

...,] 9.892886e-01 0.010711437 [4,] 9.931660e-01 0.006833979 [5,] 9.149391e-01 0.085060890 This method I have is not favorable because it just stack the matrices together as another matrix. Makes it hard to get individual matrix later. all_mat <- NULL all_mat <- c(all_mat, mat1,mat2) - Gundala Viswanath Jakarta - Indonesia

...f vector ( = 4). 3. Character "a" encode as "0", "c" -> "1", "g" -> "2", "t" -> "3" Length of strings are assumed to be uniform within the vector, and it can be greater than 3 (up to 40 characters). - Gundala Viswanath Jakarta - Indonesia

Dear all, The basename() function returns the extension also: > myfile <- "path1/path2/myoutput.txt" > basename(myfile) [1] "myoutput.txt" Is there any other function where it just returns plain base: "myoutput" i.e. without 'txt' - Gundala Viswanath Jakarta - Indonesia

...a; # Store the compressed bit into array push @data, $compressed; # process the array foreach my $dat ( @data ) { my $decompressed = unpack 'b*', $dat; $decompressed =~ s/(..)/$digmap{$1}/ge; print "$decompressed\n"; # or do further processing on $dat } __END__ - Gundala Viswanath Jakarta - Indonesia

...exp)) { sp_b <- pose+1 sp_e <- ncol(gexp) # This two doesn't do what I want part1 <- sort.gexp[posb:pose] part2 <- sort.gexp[sp_b:sp_e] # we later want to process part1 and part2 separately } } } __END__ - Gundala Viswanath Jakarta - Indonesia

...> q <- c("some", "more", "not_there") But why this failed? > extracted <- x[[q]] Error in x[[q]] : subscript out of bounds we expect the output of 'extracted' to be a vector as well. When the key is not present to give "NA" in vector - Gundala Viswanath Jakarta - Indonesia

...ery above, yielding: 0.02 0.7 However, I want to avoid slurping whole repo.txt into an object (e.g. hash). Is there any ways to do that? The reason I want to do that because repo.txt is very2 large size (milions of lines, with tag length > 30 bp), and my PC memory is too small to keep it. - Gundala Viswanath Jakarta - Indonesia

Hi, Is there a way to do it? For example I have the following vector: > print(myvector) > [1] -295.8045 -295.8045 -295.8045 -295.8045 -325.4754 -295.8045 -295.8045 [8] -295.8045 -413.2099 -295.8045 I want it to return -295.8045, which occur most often. - Gundala Viswanath Jakarta - Indonesia

Dear all, Is there any such package? I am thinking of something equivalent to Perl::Tidy. For example with VI editor one can visual highlight a portion of Perlcode and then issue the command: !perltidy then the code will be automatically arranged. - Gundala Viswanath Jakarta - Indonesia

Dear all, For example I want to process set of files. Typically Perl's idiom would be: __BEGIN__ @files = glob("/mydir/*.txt"); foreach my $file (@files) { # process the file } __END__ What's the R's way to do that? - Gundala Viswanath Jakarta - Indonesia

...07 2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC 14 3 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAT 3 But why when printint it using 'cat', it doesn't print the desired string "AAA" ? > cat(raw.count$Var1, "\n") 1 2 3 What's wrong with my cat command above. - Gundala Viswanath