similar to: Boxplot across levels of a factor

I am using dgc.genetics to perform TDT analysis on SNP data from a cohort of trios. I now have a file with about 6008 variables. The first few variables related to the pedigree data such as the pedigree ID the person ID etc. Thereafter each variable is a specific locus or marker. The variables are named by a pattern such as "Genotype.nnnnn" with nnnnn corresponding to a number which

Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here:

My data looks like this: > data name G_hat_0_0 G_hat_1_0 G_hat_2_0 G_0 G_hat_0_1 G_hat_1_1 G_hat_2_1 G_1 1 rs0 0.488000 0.448625 0.063375 1 0.480875 0.454500 0.064625 1 2 rs1 0.002375 0.955375 0.042250 1 0.000000 0.062875 0.937125 2 3 rs2 0.050375 0.835875 0.113750 1 0.877250 0.115875 0.006875 0 4 rs3 0.000000 0.074750 0.925250 2 0.897750 0.102000

Hello, I am working with a matrix of multilocus genotypes for ~180 individual snail samples, with substantial missing data. I am trying to calculate the pairwise genetic distance between individuals using the stats package 'dist' function, using euclidean distance. I took a subset of this dataset (3 samples x 3 loci) to test how euclidean distance is calculated: 3x3 subset used

Hi All- I have 24 boxplots on one graph. I do not have the whiskers extending to the outliers, but I would like to label the maximum value of each outlier above the whiskers. I have the stats but am having trouble figuring out how to label the whiskers. Any suggestions would be great! sherri

How are the lower/upper whiskers defined in the default version of boxplot {graphics}? I tried help(boxplot) and searching www.rseek.org, but I was unable to determine an absolute answer. I checked out the definition of boxplot according to Wikipedia (http://en.wikipedia.org/wiki/Box_plot), but it also had several approaches listed for how the whiskers could be determined, so I'm just

Hello, I am trying to do some simulation using the rmetasim package and I've run to this problem. --beginning of error msg-- Error in "[<-"(`*tmp*`, slice[l, ], slice[l, ], value = c(0.200000002980232, : number of items to replace is not a multiple of replacement length --end of error msg-- Here is the script I used. --script starts here-- ## load 'rmetasim'

Dear R users, I am sorry to disturb you! But I really need your help for the usage of sigPathwy. Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really

I have read and reread the boxplot and the boxplot stats page, and I still cannot understand how and what boxplot shows. I realize that this might be due to me not knowing enough statistics, but anyway... First, how does boxplot determine the size of the box? And is the line inside the box the mean or the median (or something completely different?) And how does it determine how long out the

Hi all, I've been looking in R for an EM algorithm adjusted for multiple-locus haplotypes frequencies, but failed in 100%. Has anyone heard of anything of this kind in R? Thanks in advance, Marcin

My box plot below is drawing its upper whisker all the way to the last point, instead of showing the point as an outlier. Am I misunderstanding, or is it a bug? Help(boxplot) states for the parameter ?range? that ?this determines how far the plot whiskers extend out from the box. If range is positive, the whiskers extend to the most extreme data point which is no more than range times the

Hello R-help community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus

Good Afternoon- I was wanting to alter the boxplot to remove the lower whisker, both the whisker line and staple just on the lower end. Is there a way to do this? As my code is currently: boxplot(log_loads~ind,data=nfmaum, horizontal=TRUE, notch=T, outline=FALSE, whisker=0, main="Maumee River Near Future Climate Scenarios", ylab="Log Load",xlab="Climate Scenarios")

Dear all, I am comparing: > summary(boxplot(c(1,2,3,4,5,6,7,8,50),range=1.5)) Length Class Mode stats 5 -none- numeric n 1 -none- numeric conf 2 -none- numeric out 1 -none- numeric ^^^^^ group 1 -none- numeric names 1 -none- character with: > summary(boxplot(c(1,2,3,4,5,6,7,8,50),range=0)) Length Class Mode stats 5 -none- numeric n

Hi all, I have 6 datasets(dataframes Assem_ContigsLen7 through all_ContigsLen12) containing 3 columns (contig_id, contig_length, read_count). Each dataset is composed of 3 types of contigs (assemblies of genomic fragments), 1- all Bacterial fragments, 2 - all Viral fragments, 3 - mixed fragments. I identified the type of contig through a merge with another table with just contig_id and

How to calculate the boxplots R? This question arises because we are building manually boxplots, we consulted various literature sources for calculations of the boxplot but our results differ from those generated by R, especially when calculating the whiskers. What is the procedure used by R to perform these calculations? Anyone can help us please? -- View this message in context:

Estimado Gemma Ruiz Olalla De curioso miré una búsqueda en internet, y se la comparto, de esta observe la página 8 http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf Estoy de acuerdo con Jorge y Carlos, pero por las dudas, es solo una codificación, yo sin mirar más no interpretaría que el heterocigota tiene un "peso" de 0.5, porque si hay sobredominancia, dominancia, etc

Hi, I am trying to connect points on a graph that originate from *different columns of data*. For each sample I have minimum and maximum data points and I would like to draw a line connecting these in order to visualize the spread, as well as where each sample is in relation to the x-axis. So far I can generate the points, but the only lines I have been able to make join all the minimum values

#Hello, #I have a question about obtaining results from a loop I have written. #Below is a sample of individual genotypes from a genetic question I am working on called "P.genotype.sample ". P.genotype.sample<-matrix(10,10,10) P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3) P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3) P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)

I have a data frame containing columns which are factors. I use this to make boxplots for the data, with one box per factor. I would now like to get at the data in the data frame which corresponds to the outliers. I have so far found the $out, which gives "the values of any data points which lie beyond the extremes of the whiskers", but I haven't found anything which will let me get