search for: indel

...lease a piece of help regarding the use of acast/dcast functions in reshape2 package. Specifically, I'm working with a data frame, that has information about SAMPLE, GENE, and TYPE of MUTATION (as shown below): Sample Gene Type 22M AEBP1 SNV 17M AEBP1 SNV 22M ATR INDEL 22M ATR SNV 11M BTK SNV 11M BTK INDEL I would like to transform this DATAFRAME into a MATRIX that has GENE on ROWS, SAMPLE on COLUMNS, and the elements of the matrix are SNV or INDEL (ie the types of mutations). The R code starts with : y <- data.frame(Sample = x$...

Good day, The location of indels can be retrieved from a PairwiseAlignmentsSingleSubject object by using indel. Determining any difference between the two sequences, including substitutions, is not quick nor easy. I suppose that summary displays details of the mismatches, but the variable is of class PairwiseAlignmentsSingleSubje...

Hi Do you want something like dcast(test, Sample~Gene, fun=function(x) paste(x, collapse=",")) or dcast(test, Sample~Gene, fun=function(x) sum(as.numeric(x))) 1 means INDEL, 2 means SNV and three means both Cheers Petr > -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Bogdan > Tanasa > Sent: Monday, July 3, 2017 9:22 AM > To: r-help <r-help at r-project.org> > Subject: [R] reshaping the data &g...

Hi all, I have a lengthy 'for' loop and for each loop I want to track the iteration number that is currently going on. For this, I have tried following: > for (i in 1:10) { + DumDat <- rnorm(1000) + cat("iteration:", i, " \n") + } iteration: 1 iteration: 2 iteration: 3 iteration: 4 iteration: 5 iteration: 6 iteration: 7 iteration: 8

...quot;GOOD" "DOOR" ... and I am interested in creating a matrix that contains the string edit distances between each pair of words. I am this close -> ' ' <- to writing the algorithm myself (which will allow for different variations on the string edit rules, indels, plus or minus transpositions, and possibly some variations on that), but I figured I'd see if anyone on the list has any experience with this and might already have some shoulders for me to stand on. Thanks, Thomas Thomas Hills Ph.D. Department of Psychological and Brain Sciences In...

...tions (Fabian Cenedese) > 2. Re: rsync on Windows questions (Simon Hobson) > 3. Re: rsync on Windows questions (Fabian Cenedese) > 4. Re: rsync on Windows questions (Fabian Cenedese) > > > ---------- Videresendt e-post ---------- > From: Fabian Cenedese <Cenedese at indel.ch> > To: rsync at lists.samba.org > Cc: > Date: Fri, 01 Jul 2016 09:15:30 +0200 > Subject: rsync on Windows questions > Hi > > I'm using a cygwin compiled rsync on Windows to backup > and restore files from my local Windows computer. I'm trying > several desti...

Hi, In addition to GADA, what are the available package in R and bioconductor to analyze amplification, deletion, LOH and indels of CNV, SNP data? Any reference is welcome. Best, Carol

Hi

At 10:52 02.06.2016, Hans-Christian Jehg wrote: >Content-Transfer-Encoding: 7bit > >Try having a look at this, for inspiration. > >It does require the capability of hard-links on the remote end though... and it does not resolve your "delete target directory" either, but it might save you some fiddeling around :-) >

Hi I was wondering what happens if a file that is regularly synched but seldom changes gets corrupted in the copy. As it seldom (or never) changes the mod time will always be the same. But if the content changes (bit flip, bad HD...) will rsync get this and synch it again? Would I need the -c (crc) flag for this to work? That of course slows things down quite a bit. Is this the only way to

..../../stat/html/glm.html as it should. But when I re-installed spatstat using R 1.9.0, nothing changed in this regard. I presume I could fix things by completely removing the directory containiny the installed version of spatstat and then re-installing again under R 1.9.0. But this seems a trifle indelicate. Is there a more graceful way of handling this problem? Or is there something that I should have done which would have kept this problem from arising? I had a fairly thorough read of the ``NEWS'' file and could find no relevent information. cheers, Rolf Turner rol...

yes, i`d second that. maybe you just try using metaflac to generate the appropriate list of files to sync and then feed that list to rsync. > Gesendet: Dienstag, 02. Dezember 2014 um 08:37 Uhr > Von: "Fabian Cenedese" <Cenedese at indel.ch> > An: rsync at lists.samba.org > Betreff: Re: Comparing FLAC header before syncing > > At 02:24 02.12.2014, Mike Garey wrote: > >Hi all, I'd like to modify rsync to add a flag to compare the MD5 signature of the unencoded audio data in the header of a FLAC file to deter...

Hi I'm trying to build a backup system based on rsync. It should work with different destinations (local, share, remote etc) that's why I'm looking for ways how every operation can be controlled from the client side. I want to create full backups and incremental backups. For the incremental backups I use --compare-dest lastfullbackup. This works nicely except that the whole directory

...achieved this. In which way did you connect to the database. Did you use the ADO method or ODBC DSN method to connect to the database. Please kindly guide me. Saravanan ----- Original Message ----- From: Fabian Cenedese <Cenedese@indel.ch> To: saravanan <saravananv@erdcitvm.org> Sent: Friday, February 20, 2004 5:34 PM Subject: Re: Does wine supports database applications > > >Hai all, > > I would like to know is it possible to run a Windows database application in linux using wine. For eg. How can I run...

Fabian Cenedese <Cenedese at indel.ch> wrote: >> rsync: write failed on "/Volumes/durack1ml_bak/160405_1234/Backups.backupdb/durack1ml/2016-02-10-091749/durack1ml_hdd/Applications/Adobe Media Encoder CC 2015/Adobe Media Encoder CC 2015.app/Contents/Resources/pdfl/CMaps/ETen-B5-UCS2": Result too large (34) > A...

Fabian Cenedese <Cenedese at indel.ch> wrote: > I'm having problems with the user rights. The backup works > ok but after restoring some files I can't access them. That's to be expected. NTFS has a very rich permissions system and rsync won't be capturing that. While it's a PITA, your best best is rese...

Hi Has anybody ever tried (and most probably failed) to port rsync to Win32? I know there are versions built with cygwin and there are also other Windows programs that include the rsync algorithm. But neither of them make me really happy. The cygwin version is dead slow on my AMD 3500+ and the Windows programs all make something differently, can't be scripted and/or have an unusable GUI. I

Dear R users-- I made a typo in the title after adding it to a plot, but I don't know how to delete the title. Could anyone let me know the command for that? Also, I wonder if there is any way to amend the title which already exists. Thanks, Jason [[alternative HTML version deleted]]

Hi, I'm trying to run the following program with lastest wine release. http://www.receita.fazenda.gov.br/publico/programas/irpf/2003/UnicoDisco/irpf2003v1_2.exe The installation runs OK, but when I try to run the program I got a exception. I think the problem is this fixme:file:DeviceIoControl Unimplemented control 256 for VxD device NWLINK How can I solve this? Is there any NWLINK.VXD

...ing mail in synchronization, good. But those reappearing mails make me think about switching back to 2.0.x dsync and live with the drawback of preventing mail to arrive synchronously at both servers. Is someone out there experiencing a similar behaviour with dsync 2.1.x regarding reappearing, thus indelible mail? Regards, Michael