similar to: Fixed! Thanks all:RE: scatterplot to boxplot translation?

Hello R users. This is a fairly basic question: I am concatenating data from sets of files in a directory using a loop. The column names in all files are exactly the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this:

Dear UseRs, I'm making box plots from a data set that looks like this: Chr Start End GeneDensity ReadCount_Explant ReadCount_Callus ReadCount_Regen 1 1 1 10000 107.82 1.243 1.047 1.496 2 1 10001 20000 202.50 0.835 0.869 0.456 3 1 20001 30000 158.80 1.813 1.529 1.131

Thanks to both Weidong and David for the help! By implementing both of your suggestions I was able to make this work. I did end up putting header=TRUE for both read operations. --Kelly ________________________________________ From: David Winsemius [dwinsemius at comcast.net] Sent: Tuesday, August 30, 2011 1:16 PM To: Vining, Kelly Cc: Weidong Gu; r-help at r-project.org Subject: Re: [R] column

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Thanks for your help, Rui! That works and will save me a lot of trouble. --Kelly -----Original Message----- From: Rui Barradas [mailto:ruipbarradas at sapo.pt] Sent: Tuesday, July 10, 2012 2:24 AM To: Vining, Kelly Cc: r-help at r-project.org Subject: Re: [R] boxplot with "cut" Hello, Maybe this iss what you're looking for. GD is your data.frame. multi.boxplot <-

Hello R users, I have a set of data frames for which I am tallying row numbers, as shown below. > nrow(mC_Explant) [1] 14480 > nrow(mC_Callus) [1] 23320 > nrow(mC_RegenPlant) [1] 8108 etc. I want to create a new data frame which has the variable names as column headings, and then a single row with the nrow tallies. My first step was this: dfIntron <- c(nrow(mC_Explant),

Dear R users, I am running the following code below, the gem751be.rpkm is a dataframe with dim of 751 samples by 35164 variables, 73 phenotypic variables in the furst to 73rd column and 35091 genomic variables or genes in the 74th to 35164th columns. What I need to do is to calculate the residuals for each gene using the simple linear regression model of genelist[i] ~ purity2; The following

Dear useRs, I have a slightly complicated data structure and am stuck trying to extract what I need. I'm pasting an example of this data below. In some cases, there are duplicates in the "gene_id" column because there are two different "sample 1" values for a given "sample 2" value. Where these duplicates exist, I need to average the corresponding

Hello, I'm seeing three different vignette-related errors with recent versions of R-3.0.0 alpha. First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ?BitSeq.Rnw' failed with diagnostics: Failed to locate the ?weave? output file (by engine ?utils::Sweave?) for

Dear useRs, A colleague has sent me several batches of output I need to process, and I'm struggling with the format to the point that I don't even know how to extract a test set to upload here. My apologies, but I think that my issue is straightforward enough (for some of you, not for me!) that you can help in the absence of a test set. Here is the scenario: # Data sets are lists: >

Dear UseRs, I have a data frame that looks like this: head(test2) attributes start end StemExplant Callus RegenPlant 1 LTR_Unknown 120 535 3.198 1.931 1.927 3 LTR_Unknown 2955 3218 0.541 0.103 0.613 6 LTR_Unknown 6210 6423 6.080 4.650 9.081 9 LTR_Unknown 9658 10124 0.238 0.117 0.347 14 LTR_Unknown 14699 14894 3.545 3.625

Thanks Don and Jim, "Get" did the trick! That command is new to me, and is exactly what this problem needed. The syntax that worked is actually slightly simpler than what was suggested. This is what worked: all.comps <- ls(pattern="^res") for(i in all.comps){ obj = get(i); ... Thanks again. --Kelly V. -----Original Message----- From: MacQueen, Don [mailto:macqueen1 at

Hi all, I have been struggling with this problem for a few days. I have a data table like this: gene rpkm1 diff1 rpkm2 diff2 gene1 23 50 13 120 gene2 111 220 827 1200 gene3 75 998 71 910 And I want to re-format it so that, for each gene, I have a 2x2 contingency table, such as: gene rpkm diff gene1 23 50 gene1 13 120 gene2 111 220 gene2 827

Thanks again for your help. I did indeed solve the problem by plotting the initial graph as type='n', then adding my subset of points using 'points'. Cheers, --Kelly V. -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Dallas Sent: Friday, February 24, 2012 5:58 AM To: r-help at r-project.org Subject: Re: [R]

Dear useRs, I'm having trouble with what is likely a very simple issue with a simple graph. I have data in the format pasted below - total from which this is a subset is > 3 million rows. I'm plotting "Window" on the x axis, and either of the other two columns on the y axis. In both the second and third columns, the values are in a range from 0 to 1. I want to be able to plot

Folks, I am having major performance issue with my Erlang application running on openstack KVM hypervisor and after so many test i found something wrong with my KVM guest CPU Topology This is KVM host - http://paste.openstack.org/show/790120/ This is KVM guest - http://paste.openstack.org/show/790121/ If you carefully observe output of both host and guest you can see guest machine threads has

Hi all, In short: I'm running ddply on an admittedly (somehow) large data.frame (not that large). It runs fine until it finishes and gets to the "collating" part where all subsets of my data.frame have been summarized and they are being reassembled into the final summary data.frame (sorry, don't know the correct plyr terminology). During collation, my R workspace RAM usage goes

I am getting an error message from scatterplot: > library(car) > scatterplot(Prestige$income~Prestige$type) Error in Summary.factor(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, : range not meaningful for factors In addition: Warning message: In Ops.factor(x[floor(d)], x[ceiling(d)]) : + not meaningful for factors > The command does output the kind of graph that I want (boxplots).

Hello- I'm new to R, coding and stats. (Oh no.) Anyway, I have about 12000 data points in a data.frame (dealing with dimensions and geological stage information for fossil protists) and have plotted them in a basic scatter plot. I also added a boxplot to overlay these points. Each worked fine independently, but when I attempt to superimpose them with add=true, I get a different scale for

I am running R version 2.15.1 in Windows XP I am having problems with a function I'm trying to create to: 1. subset a data.frame based on function arguments (colname & parmname) 2. rename the PARMVALUE column in the data.frame based on function argument (xvar) 3. generate charts plotvar <- function(parentdf,colname, parmname,xvar,yvar ){ subdf <-