similar to: help

Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: > peaksWithSequences <- getAllPeakSequence(peakList, upstream = 100, > downstream = 100, genome = Hsapiens) Error in validObject(.Object) : invalid class "GRanges" object: superclass

I have a bunch of benchmark measurements that look something like this: sample.1 0.0000066660 0.0000062500 0.0000058330 0.0000058330 0.0000058330 sample.2 0.0000058330 0.0000058330 0.0000058330 0.0000058330 0.0000058330 sample.3 0.0000062500 0.0000062500 0.0000070830 0.0000062500 0.0000066660 i.e each measurement take on one of a set of values. The set values isn't fixed, but

Dear R users, I am currently working in subsetting a zooreg() object using either window or subset. I have a solution but it may be a bit cumbersome when I start working with actual data. Your inputs would be greatly appreciated. Example: I have a zooreg() object that starts in 1997 and ends in 2001. This object contains daily data for the 4 years

This has got to be incredibly simple but I nevertheless can't figure it out as I am apparently brain dead. I just want to convert the elements of a character vector to variable names, so as to then assign formulas to them, e.g: z = c("model1","model2"); I want to assign formulas, such as lm(y~x[,1]) and lm(y~x[,2]), to the variables "model1" and

Hello R-Users I am struggling with this line plot, it might be simple but I am missing something here. First of all I want to make multiple line plots across seasons (DJF,MAM,JJA,SON) for 12 variables (here, called nodes) and fill them with the node. So that season=x-axis, node=line col and freq=y-axis. My plot currently links all DJFs, MAMs, JJAs and SONs, however I will like them to be

Dear list members, I have got another problem. I imported an SPSS file with the Memisc package using the following commands: mz <- spss.system.file("myspssfile.sav") mz <- subset(mz,select=c( bsex,balt,xurb,dtaet,kartab,bgeb,boseit,bgeblan,xnuts2,kausb,xerwstat, asbper,asbhh,ajahr,aquartal,bstaat,xwieoft,gew1,apkz,bpkzm,bpkzv)) Afterwards I checked the measurements of the

Dear all Im new in R I have a necdf data set that I want to plot : this is my data set [1] "file Tmax.DJF.daily.1981_1999.echama2.nc has 4 dimensions:" [1] "longitude Size: 127" [1] "latitude Size: 110" [1] "ht Size: 1" [1] "t Size: 1680" [1] "------------------------" [1] "file Tmax.DJF.daily.1981_1999.echama2.nc has 1

Hi all, I have made a plot with ssplot, using a SpatialPointsDataFrame. The content is quite simple, as I have 9 grid points with lon/lat coordinates and 9 values attached to these coordinates. They are in a square area of 3 by 3 gridboxes. I would like to lay a map from maps() over these values, but when I try this, the grids of the maps (smaller) do not overlap with the grids I have

I am trying to extract only the winters (defined to be 01-Dec through 28-Feb) of daily data from 1948-2002. There are 90 days in each winter season. I wrote the following code to gather the winter dates into a single vector: DJF <- NULL for(year in 1949:1999) { temp.begin <- strptime(paste("01/12", year-1, sep="/"), "%d/%m/%Y") temp.end <-

Dear all, I would like to know if I can compare by a significance test 2 models with different kind of parameters. Perhaps I am wrong but I think that we can only compare 2 models if one is a sub model of the other. Med venlig hilsen / Regards João Fadista Ph.d. studerende / Ph.d. student AARHUS UNIVERSITET / UNIVERSITY OF AARHUS Det Jordbrugsvidenskabelige Fakultet / Faculty of

Dear all, I would like to know how can I concatenate 2 data.frames into a single one. Both data frames have the same number of columns and the same class type in each correspondent column. So what I want is to have a new data.frame where I have first the values from one data.frame and then the values from a second data.frame would came after in this new data.frame. Thanks in advance. Med

Hi all, I've got a list of files from 1914 to 2000. For each file, I can call the read.table function as follows. > file <- read.table("1914.txt") But I want to make a script so that at the end of the loop, the script selects the file 1915.txt, 1916.txt and so on. I've used seq() to create the increment seq <- paste(seq(1914, 2006, by=1), "*.txt.h",

I admit that I've not done a thorough search on this topic, but from the several instructional manuals and/or tutorials I've looked at, I don't see any mention of relational database capabilities in R? Have I missed something, and if so, can someone point me in the right direction to get started? Thanks! Jim Bouldin, PhD Research Ecologist Department of Plant Sciences, UC Davis

I realize this is probably pretty basic but I can't figure it out. I'm looping through an array, doing various calculations and producing a resulting data frame in each loop iteration. I need to give each data frame a different name. Although I can easily create a new character string for writing each frame to an output file, I cannot figure out how to convert such strings to

I'm trying to run this simple random sample procedure and keep getting the error message shown. I don't understand this; I've designated x as a numeric vector, so what is going on here? Thanks. > x = as.vector(c(1:12));x [1] 1 2 3 4 5 6 7 8 9 10 11 12 > mode(x) [1] "numeric" > sample(x, 3) Error in sample(x, 3) : .Random.seed is not an integer vector

I'm trying to obtain the mean of the middle 95% of the values from each row of a matrix (that is, the highest and lowest 2.5% of values in each row are removed before calculating the mean). I am having all sorts of problems with this; for example the command: apply(matrix1,1,function(x) quantile(c(.05,.90),na.rm=T)) returns the exact same quantile values for each row, which is clearly

I can't seem to find info on how to unload packages that have been loaded. My goal in doing so is to gain access to functions that have been masked out by those packages. Or is there another way to do so? Thanks in advance. Jim Bouldin, PhD Research Ecologist Department of Plant Sciences, UC Davis Davis CA, 95616 530-554-1740

I realize this should be simple but I'm having trouble subsetting vectors and matrices, for example extracting all values meeting a certain criterion, from a vector. Cannot seem to figure out the correct syntax and help page not very helpful. Or should I be using some other function than subset. Thanks for any help. Jim Bouldin

When I try to run the following non-linear regression with variables index1 and prl3: > beta = 4 > nls(index1~beta*(1/prl3),start = list(beta = 4)) I get this error message: Error in nls(index1 ~ beta * (1/prl3), start = list(beta = 4)) : REAL() can only be applied to a 'numeric', not a 'logical' I've got no clue as to the REAL() to which this is referring. Any

Is there a command for partial matching of character strings? Specifically, I'd like to be able to calculate the mean of the values in any columns in a data frame or matrix that have identity in part of their column names. For example, columns labeled "mpw06a" and "mpw06b" match on the first five characters; their mean would be taken whereas any columns beginning with