similar to: Documenting variables, dataframes and files?

In my orgainzation, the people resonsible for the network are not that keen on setting up new software, so when I asked them to set up emacs or some other common R editor, I was told to have a look at ConText. This editor is avaliable in the network, and there is some R support. Special commands are highlighted and such, but the most important part, sending commands writtten in a ConText window

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

Hi, I am having troubles with creating an eSet and would appreciate any help on the following problem. I am trying to create an eSet using the following code pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type =

Utilizo la función merge desde hace poco, pero no se me ocurre cómo utilizarla para esto. Yo pienso que se puede hacer con una combinación de ifelse-s pero no sé cómo. Seguro que hay más de una forma ce hacerlo. Quoting José María Mateos <chema en rinzewind.org>: > On Sat, Nov 10, 2018 at 07:54:19PM +0100, Manuel Mendoza wrote: >> Muy buenas. A ver si alguien puede echarme

Muy buenas. A ver si alguien puede echarme una mano. A partir de una matriz de distancias de 29 x 29 he obtenido una df1. Ahora tengo 841 filas con la distancia de cada combinación de esas 29 categorías. Algo así como: Var1 Var2 Dist a a 0 a b 3 a c 5 b a 3 b b 0 b c 5 c ... En otra df2, de 14563 filas, tengo las

Hi, I'm very confused about R structures and the methods to go with them. I'm using R for microarray analysis with Bioconductors. Suppose without reading the documentations, what's the best way to explore a data structure when you know nothing about it? I am currently using is() / class() to see what the object is. str() / attributes() to probe inside the object, and

#I want to "merge" or "join" 2 dataframes (df1 & df2) into a 3rd (mydf). I want the 3rd dataframe to contain 1 row for each row in df1 & df2, and all the columns in both df1 & df2. The solution should "work" even if the 2 dataframes are identical, and even if the 2 dataframes do not have the same column names. The rbind.fill function seems to work. For

Hello, I'm wondering how I can merge two featuresets into one. My dataset is two sets of microarray data and it looks like followings: > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59

Hello, I have two dataframes DF1 and DF2 that should be identical but are not (DF1 has some rows that aren't in DF2, and vice versa). I would like to produce a new dataframe DF3 containing rows in DF1 that aren't in DF2 (and similarly DF4 would contain rows in DF2 that aren't in DF1). I have a solution for this problem (see self contained example below) but it's awkward and

Hi there, I have a list of dataframes (generated by reading multiple files) and all dataframes are comparable in dimension and column names. They also have a common column, which, I'd like to use for merging. To give a simple example of what I have: df1 <- data.frame(c(LETTERS[1:5]), c(2,6,3,1,9)) names(df1) <- c("pos", "data") df3 <- df2 <- df1 df2$data

Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name ("FileName" instead of "Filename") which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers

Gracias a los tres, Raúl, Marcelino y Carlos. Lo del "get" de Marcelino me da la respuesta a lo que yo exactamente preguntaba, y funciona, pero ahora tengo problemas con el for, por lo que probablemente recurra al eval parse de Raúl o Carlos, que ya tienen el for. Aún así, lo intento 1º con el get. Con subset(df, subset=get(GT[i])>0) el problema es que en el for hago un

Subsetting from a dataframe with only one variable returns a vector, not a dataframe. This seems somewhat inconsistent. Wouldn't it be better if subsetting would respect the structure completely? v1<-1:4 v2<-4:1 df1<-data.frame(v1) df2<-data.frame(v1,v2) sel1<-c(TRUE,TRUE,TRUE,TRUE) > df1[sel1,] [1] 1 2 3 4 > df2[sel1,] v1 v2 1 1 4 2 2 3 3 3 2 4 4 1 -- Erich

Hallo Everyone I have the kind of problem that one should never have because one must always plan well and communicate with your team. But now I haven't so here is my problem. I have data coming in on a daily basis from surveys in 10 towns. The questionnaire has 62 variables but some of the regions have used older versions of the questionnaire that have a few variables less. I want to combine

Hi all, I am not a skillful R programmer and has I am handling with large dataframes (about 30000 x 300) I am in need of an efficient function. I have 4 dataframes with the same dimension. I need to generate other dataframe with the some dimension than the others where in each position it has the median value of the 4 values in the same position coming from the 4 dataframes. Grateful by your

Hi, R-listers, Failed, when I tried to merge df1 and df2 by "codetot" in df1 and "codetoto" in df2. I want to know the reason and how to merge them together. Data frames and codes I have used were listed as followed. Thanks a lot in advance. df1: popcode codetot p3need BCPy01-01 BCPy01-01-1 100.0000 BCPy01-01 BCPy01-01-2 100.0000 BCPy01-01 BCPy01-01-3 100.0000 BCPy01-02

If I save a dataframe with a character-typed last column to a relational database with dbWriteTable, the values in the last column of the resulting table in the database will have a '\r' (carriage return) appended. If I read back the dataframe with dbReadTable the last column in the resulting dataframe has also '\r' appended (see protocol below). Setting or unsetting sql-mode

Hi, I'd like to merge mutliple dataframes from a list of dataframes by some common columns. The approach for simply merging 2 dataframes is working with: merge(df1,df2,by=c("col1","col2","col3"),all=TRUE) For mutliple dataframes in a list I try to use the merge_all command from the package reshape. The documentation states that the command takes a list of

Dear All Sorry for this simple question, I could not solve it by spending days. My data looks like this: # data set.seed(1234) clvar <- c( rep(1, 10), rep(2, 10), rep(3, 10), rep(4, 10)) # I have 100 level for this factor var; yvar <- rnorm(40, 10,6); var1 <- rnorm(40, 10,4); var2 <- rnorm(40, 10,4); var3 <- rnorm(40, 5, 2); var4 <- rnorm(40, 10, 3); var5 <- rnorm(40, 15,

Gracias Marcelino. Si, (i in 1:length(GT)), lo he utilizado mil veces, pero se me sigue olvidando de una vez a otra. Lo iba a mirar, pero me centré primero en que me hiciera bien el mapa. He probado el for y me da este error: Error in aes(x = lon, y = lat, color = get(GT[i]), size = 2) + scale_colour_gradient(low = ("white"), : non-numeric argument to binary operator