similar to: Histogram for each ID value

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 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

I've been looking for how to change a certain percentage of values in a data frame, but I've been struggling to find information in R. For example: #################example data############## > data V1 V2 V3 V4 V5 V6 V7 1 chr1 500 500 CHH 0 0.5 + 2 chr1 550 550 CHH 0 0.0 + 3 chr2 700 700 CHH 0 0.0 + 4 chr2 1000 1000 CHH 0 0.0 + 5 chr3

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")

Hello, I'm a new R user. I have two different dummy tables with the variable name tb1 and tb2. tb1< v1 v2 v3 v4 "chr1" 22 23 3 "chr1" 36 37 1 "chr1" 54 55 0 "chr1" 77 78 1 "chr2" 80 81 4 "chr2" 85 86 0 "chr2" 99 100 1

Hi Jim I am trying to prepare a bed file to load as accustom track on the UCSC genome browser. I have a data frame that looks like the one below. > x V1 V2 V3 1 chr1 11255 55 2 chr1 11320 29 3 chr1 11400 45 4 chr2 21680 35 5 chr2 21750 84 6 chr2 21820 29 7 chr2 31890 46 8 chr3 32100 29 9 chr3 52380 29 10 chr3 66450 46 I would like to insert the following 4 lines at the beginning:

Hello, I have an input file: http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt where col 1 is chromosome, column2 is start of region, column 3 is end of region, column 4 and 5 is base position, column 6 is total reads, column 7 is methylation data, and column 8 is the strand. I would like a summary output file such as:

If row numbers can be dispensed with, then tidyr makes this easy with the unnest function: ##### library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union library(purrr)

Hi Peter I have the following data frame with chromosome name, start and end positions: chrN start end 1 chr1 11122333 11122633 2 chr1 11122333 11122633 3 chr3 11122333 11122633 8 chr3 111273334 111273634 7 chr2 12122334 12122634 4 chr1 21122377 21122677 5 chr2 33122355 33122655 6 chr2 33122355 33122655 I would like to count the positions that have the same start and

Hi Bogdan, Messy, and very specific to your problem: df.sample.gene<-read.table( text="Chr Start End Ref Alt Func.refGene Gene.refGene 284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194 465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910 525 chr2 223777758 223777758 T A

I would appreciate please a suggestion on how to do the following : i'm working with a dataframe in R that contains in a specific column multiple gene names, eg : > df.sample.gene[15:20,2:8] Chr Start End Ref Alt Func.refGene Gene.refGene284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194465

I want to remove the column names from a data frame. I do it the long way, can any body show me a better way ? df= data.frame(chrN= c(“chr1”, “chr2”, “chr3”), start= c(1, 2, 3), end= c(4, 5, 6), score= c(7, 8, 9)) df #I write a txt file without row or column names write.table(df,"df1.txt",sep='\t',quote=FALSE,row.names=F,col.names=F) #then I read it with the header = F

Dear all, I have the following data frame: V1 V2 aaa chr1 aaa chr2 aaa NM aaa QC aaa chr10 att NM att chr7 What I want to do is to count the string (V1). But the condition of counting is: if the V2 of the string is "NM" or "QC" then the count is not increased. Hence the contigency table will look like this: #tag count aaa 3 att 1 Is

I have the following xyplot figure: http://img577.imageshack.us/img577/686/filesizeresults12000000.png The data are organized in a matrix file as follows: Type Elements Chromosome Time bedGz 12000000 chr1 14.240 bedGz 12000000 chr2 7.949 bedGz 12000000 chr3 5.103 bedGz 12000000 chr4 5.290 bedGz 12000000 chr5 5.161 ... The x-axis labels in the Chromosome column are ordered

Hi all, I'm trying to use the package read.table within a foreach loop. I'm grabbing 500M rows of data at a time from two different files and then doing an aggregate/tapply like function in read.table after that. I had planned on doing a foreach loop 39 times at once for the 39 files I have, but obviously that won't work until I figure out why the segfault is occurring. The

Dear all, please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. : " args <- commandArgs(TRUE) TUMOR <- args[1] GERMLINE <- args[2] CHR <- args[3] ". when I submit the R script to a PBS HPC scheduler, I do the following (below), but ... I am getting an error message. (I am not posting the error message,

Hello I have a data frame and one of its columns is as follows: Col chr1:71310034 chr14:23354088 chr15:37759058 chr22:18262638 chrUn:31337214 chr10_random:4369261 chrUn:3545097 I would like to get rid of colon (:) and replace this column with two new columns containing the terms on each side of the colon. The new columns should look as follows: Col_a Col_b chr1

This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC

Hi, The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub. Unfortunately we don't use qsub anymore so can't test it, but it should be as follows: R-script eg. test.R: > ##First read in the arguments listed at the command line > args=(commandArgs(TRUE)) > > ##args is now a list of

Hi, List, Sorry in advance if this turns out to be a stupid question -- I've been trying to work it out for awhile, and I don't have any new ideas -- I'm very new to R documentation/ LATEX. I am running "R CMD check " on a package that I am trying to write; the only warning is: * checking for missing documentation entries ... WARNING Undocumented data sets: Einter KG All