similar to: Looping over files

Dear list, I wish to plot chromatin precipitation data: I would like to have a rectangles (x:end-start, y:peak) but I do not have an idea how to define x (in terms of qplot syntax) and to choose the correct geom. mydata is a subset of a larger file. > mydata chrom start end peak 1 chr11 5291000 5291926 8 2 chr11 10988025 10988526 7 3 chr11 11767950 11768676 8 4

Greetings, I am new to R, but trying to put in the time to learn. I have read the R manual and several other introductory texts; however, there is nothing like actually putting it into practice. So here is my problem, and its more of a learning exercise for myself than anything else, but I'm stuck and getting extremely frustrated that I can't figure it out. I'm trying to make a

Dear all, I've fitted a lm using 61 data (training data), and I'left 10 as test data. Training data and test data are stored in an excell. training <- read.xls("C:/...../training.xls") , the same for test. That is: v1 v2 ... v15 When I type str(training) and str(test), both sets have the same names The resulting model is lms <- lm(vd ~ log(v1) + fv2+ fv5+ fv7 )

Hi, I have a dataset that looks like the one below. data plot plantno. species H 31 ABC D 2 DEF Y 54 GFE E 12 ERF Y 98 FVD H 4 JKU J 7 JFG A 55 EGD . . . . . . .

Hi, I've been trying to use the impute2mach function in the GenABEL library. I unfortunately cannot make a working example as when I scale down the files I no longer get an error message. The error message that I get on the full file is: Error in checkSlotAssignment(object, name, value) : assignment of an object of class "NULL" is not valid for slot "data" in an

Hello. I'm very happy with libvirt and qemu, that great software! (after some playing i want to create golang bindings to libvirt).. Now i provide ext4 fs for qcow2 images (raid1 with two sata disks). Now i don't need live migration (but may need it in feature). What is the best way to provide disks to vm in case of performance, ability to create backups (i don't want lvm snapshots)?

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

Dear All My server got inconsistency from sudden power cut that I fixed it with #fsck -fvy /dev/hda at the maintenance prompt . But after reboot, one of the installed applications is preventing it from booting up (as can be seen in the boot up process list). Can you please let me know how can I remove it from the boot up list to reach the root user prompt and then re-install it again ? Thank you

CRAN (and crantastic) updates this week New packages ------------ * apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code published by Frey and Dueck. * BioPhysConnectoR (1.6-1) Franziska Hoffgaard

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })

Thomas, Thank you for your reply about the for () loop. The as.character advice worked. Sorry for the delay in getting back to?I had to set the project aside for a few weeks. This didn?t work exactly as is for (patient in as.character(1:n)){ pt <- MRN == patient (rest of the function) } But this did for (patient in as.character(levels(MRN))){ pt <- MRN == patient (rest of the function)

--Apple-Mail-7--233789088 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Kurt I currently have on my Mac gcc 2.95.2, 3.1, and 3.3 and the corresponding g77 versions as well. R builds fine with the 2.95.2 combo, it also builds fine with gcc 2.95.2 and g77 3.1. But using gcc 3.1 or gcc 3.3 gives the familiar problem that I mentioned before (although

Dear All My CentOS server got file system inconsistency , asking for "type Ctrl-D for normal boot or give root password for maintenance to run fsck manually". I tried for manually run fsck , as the followings : #fsck -s /dev/hda3 But after rebooting the server it will come back again at the similar prompt asking for "give root password for maintenance" . Can you please do me

CRAN (and crantastic) updates this week New packages ------------ * allan (1.0) Alan Lee http://crantastic.org/packages/allan Automates Large Linear Analysis Model Fitting * andrews (1.0) Jaroslav Myslivec http://crantastic.org/packages/andrews Andrews curves for visualization of multidimensional data * anesrake (0.3) Josh Pasek http://crantastic.org/packages/anesrake This

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