similar to: find common regions between two kinds of tests

Hi, Am am plotting aggregated frequency data (extracted from an RDBMS) relating to DNA sequence features for each of the human chromosomes as described in the table chromosomes below (the frequency data is in a table 'hits' that has a value (or not) for each of a set of bins across each chromosome). I would like to mark the extent of the chromosome (according to the length value in

> chromosomes id refseq name length 1 0 NC_000001.9 Homo sapiens chromosome 1 247249719 2 1 NC_000002.10 Homo sapiens chromosome 2 242951149 3 2 NC_000003.10 Homo sapiens chromosome 3 199501827 4 3 NC_000004.10 Homo sapiens chromosome 4 191273063 5 4 NC_000005.8 Homo sapiens chromosome 5 180857866 6 5 NC_000006.10 Homo sapiens chromosome 6

Hello, I have an R script that I use as a template to perform a task for multiple files (in this case, multiple chromosomes). What I would like to do is to utilize a simple loop to parse through each chromosome number so that I don't have to type the same code over and over again in the R console. I've tried using: for(i in 1:22){ etc.. } and replacing each chromosome number with

I am attempting to sample 10 markers from each chr, with a maximum distance of 14, calculated by the location of the marker in each chromosome as loc[i+1] - loc[i]. I presume the easiest way to do this is with a while loop, so that the function keeps resampling when the max distains is greater than 14. Example code is below. I have gon as far as to select markers and calculate the distances, A

Dear R-Helpers, I am not very experienced in using lattice and I am still in the learning stage I have a data set which looks like this: (I have deleted a few lines in order to save space) Chromosome marker Marker.Name Distance 1 1 1 PeMm261 0.0000 2 1 2 Xtxp8 10.1013 .. 20 1 20 EbMi148 210.3099 21 1 21 Xtxp25

Dear R community, I need to plot the results of some simulations I did using QTL Cartographer. I am plotting LOD scores over three chromosomes. The three plot have to be one next to the other. The procedure I am using is: par(mfrow=c(1,3)) plot(x$x, x$y, ylim=c(0,35), type="l", col="blue", las=1, xaxs="i", yaxs="i", xlab="X Chromosome",

Dear all. I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against chromosome and physical location within each chromosome in one plot. The data matrix looks as below: chr location copy_num 1 118345 1.320118 1 3776202 1.133879 1 4798845 0.989997 1 5350951 1.100967 . more data here . . 2 118345 2.459119 2 157739 1.915919 2 1530065 1.924372 2

Hi R-ers, I am struggling with my x-axis in a association plot. What I would like is to place the labels of the x-axis between the tick markers and normally the labels are printed at the place where the tick marker is placed. I don???t want to move the tick marker (it gives the switch between one chromosome and the next) but I just want to put the chromosome number in between the

Hello, I have a list with gene names, fold changes (=expression level) and chromosomes. Names fold change chromosome hz 1.5 2 If I plot fold change versus chromosome (or vice versa): plot (ch, fc) I see only the chromosomes with numbers but not those with letter (x and y). What can I do? A second question: How can I add a single line in that plot at a certain

mcga 1.1 (machine coded genetic algorithms) package implements a genetic algorithm optimisation tool with machine coded chromosomes. The machine coded chromosomes stand for chromosomes that are not decoded and encoded. The byte representation of 'double' type variables are crossed-over and mutated. This is different from the binary coded and real coded genetic algorithms. Linux and

mcga 1.1 (machine coded genetic algorithms) package implements a genetic algorithm optimisation tool with machine coded chromosomes. The machine coded chromosomes stand for chromosomes that are not decoded and encoded. The byte representation of 'double' type variables are crossed-over and mutated. This is different from the binary coded and real coded genetic algorithms. Linux and

Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, > chromosome <- c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) >barplot (chromosome, col="purple", xlab="Oryza sativa Chromosomes", border = NA, space =

Hi, I would like some extra information on the 'cgh' package in R. I noticed that there isn't much activity regarding this package on the R and BioC mailing list (I googled it). I started using this package and I have few questions: 1/ As I have a custom tiling like array @8um features resolution (affy), I have a lot of probes to work with. I'm assuming it is correct to

I have two datasets that I would like to plot in a single figure. The first plot is generated by a function that then takes a subset of the data. (It is biological data so it is usually by chromosome e.g. function(data1,subset="chr8") ) Since not only are the chromosomes different sizes, but across different datasets there may be different numbers of points for a single chromosome, I

Hi there, First off, despite this being my first post here, I have scanned the R help forums a lot in the past few months to help with some questions, so a big thank you to the community as a whole for being so helpful! I'm somewhat of an R newbie, and have run up against a problem that I can't seem to solve. If anyone is able to help I would really appreciate it! I'm looking at a

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, SETUP: I have pairwise data on 22 chromosomes. Data matrix X for a given chromosome looks like this: 1 13 58 1.12 6 142 56 1.11 18 307 64 3.13 22 320 58 0.72 Where column 1 is person ID 1, column 2 is person ID 2, column 3 can be ignored, and column 4 is how much chromosomal sharing those two individuals have in some small portion of the chromosome. There are 9000 individual people, and

> On Apr 19, 2018, at 1:22 PM, David Winsemius <dwinsemius at comcast.net> wrote: > > >> On Apr 19, 2018, at 11:20 AM, Ding, Yuan Chun <ycding at coh.org> wrote: >> >> Hi All, >> >> I want to create a categorical variable, cat.pfoa, in the file of pfas.pheno (a data frame) based on log2pfoa values. I can do it using the following code.

Dear R-listers, I want to reperfrom a poisson distribution test that presented in a recent-published biological research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes. For instance: The observed gene number in chromosome A is 36. The expected gene number in chromosome A is 30. Then, the authors got a

I have a data frame (narrow) with 431 rows and 6 columns containing information on chromosome, position, lod1, lod2, lod3, lod4, looking like this: > narrow chr pos lod1 lod2 lod3 lod4 1 1 3.456 -0.025 -0.003 -0.209 -0.057 2 1 5.697 -0.029 -0.005 -0.200 -0.058 3 1 8.434 -0.049 -0.012 -0.247 -0.092 4 1 9.466 -0.074 -0.025 -0.300 -0.136 5 1 9.706