similar to: possible reason for merge not working

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

Hi Is it possible to open a connection to an FTP site such that I can read the directory listing? Eg: URL <- url("ftp://ftp.ensembl.org", open="r") Error in url("ftp://ftp.ensembl.org", open="r") : unable to open connection URL <- url("ftp://ftp.ensembl.org") open(URL) Error in open.connection(URL) : unable to open connection I think

Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem

Dear All, I have built a package which has a data.frame "annotIndex.rda in its "data" folder. I am using this data frame within two functions in my package. Though my package works fine, yet when I do a R CMD check to my package I get the following two notes get.affy.ensembl: no visible binding

Dear list, I am having a set of human oligo ids (H200006022 H200002025 H300004703 H200000442 H200005719 H300018350) which I want to map to Ensembl or RefSeq. I am sure R has a function to do that. I downloaded the {oligo} package and tried to use the probeNames function. Although the factor of ologo ids is an object (as the argument to probeNames should be) I retrieve the following error:

Hi ! >From an Ensembl annotation like ENSGxxxx /// ENSGyyyyy /// ENSGzzzz, I am trying to keep only the first part: ENSGxxxx. I wasn't able to find any helpful information about how to do it. Could you help me with that please ? Is the use of the equivalent to the Excel * (any text) a good way of doing it and how ? Your help will be very much appreciated. Amelie [[alternative

Hi all, I have two data frames, two columns each, 1000s of rows. Each row represents a segment of the genome where a deletion has occurred. First column is start position of the deletion in genomic distance, second is end position. So, e.g., first 3 rows of data frame A is: 1003 1023 5932 6120 12348 12689 first 3 rows of data frame B is: 852 5305 1010 1015 8500 9500 10000 13000 I want to merge

I'm trying to identify the positions of all genes within a specific chromosomal region using biomart. When using the current biomart database I'm able to do this without issue. However, I need to use build 36 of the mouse genome which was last included in ensembl mart 46. I selected this mart and the mouse dataset as follows: mart<-useMart(biomart="ensembl_mart_46",

Amigos de la erre. He creado mi primer bucle con for para entrenar unos modelos con GAM. La respuesta es quasipoisson porque estoy trabajando con densidades de peces. Sin embargo, tengo un problema, no se muy bien como añadir el offset a la formula siguiente cuando creo el bucle. GAM.A1 <-gam ((DYO)~s(DMA,k=4)+ s(WOD,k=4)+s(CIN,k=4)+s(DRA,k=4)+s(DBR,k=4)

Dear R colleagues, I annotated a list of single nuclotide polymorphiosms (SNP) with the corresponding genes using biomaRt. The result is the following data.frame (pasted from R): snp ensembl_gene_id 1 rs8032583 2 rs1071600 ENSG00000101605 3 rs13406898 ENSG00000167165 4 rs7030479

Steffen, When the new biomaRt tries to load it errors out because I do not have RMySQL installed. There is not a Windows binary for RMySQL and it does contain C code that I do not know how to build. I do not use the MySQL option in biomaRt. Does RMySQL need to be a required dependency? Below is my screen output and sessionINfo. require(biomaRt) Loading required package: biomaRt Loading required

Hola, buen día. Una consulta, no sé conozco en extenso todas las bondades de R, pero quería saber exactamente si hay algún paquete que permita realizar análisis ecológicos específicamente para comunidades marinas. Existen muchos índices, indicadores, estimadores en general en muchos programas que están a nivel de usuario, pero quería saber si todos estos pueden estar ya disponibles en R.

Buenos días. Tengo dos mapas que hago con ggplot (abajo) y necesito superponer el 2º al 1º. En el 1º se representa la variable PA, binomial (0, 1), en gris, y en el 2º la variable ExtTG7085, que es numérica y va de 0 a 200. La 2ª es un gradiente en rojo. Lo ideal sería que donde coinciden el rojo de la 2ª se viera más oscuro, pero supongo que eso no es fácil. Podría también ser en otro color, pero

I have an issue where at odd times, maybe after 3 days, maybe after a week, people suddenly cant do domain logons. Unfortunately the machine is 50km away so i'm sure theres more details I can glean once I can interogate the users a bit more. Things I have noticed: Anyone currently logged in can still work fine. A restart of samba fixes the issue (till it hapens next). ps ax shows smbd and

Buenos días. Hago mis mapas con el código que os copio abajo, pero me gustaría que me dibujase las líneas del mapa después de poner los puntos para que se vean. Puedo hacer los puntos más pequeños, pero entonces quedan separados y yo quiero que rellenen el mapa. Gracias, como siempre, Manuel print(ggplot(legend=FALSE)+geom_path(data=map_data('world'), aes(x=long,

Dear all, I have a data which is in text file and i would like to import the data to R. From the manual, i?ve found the read.table command function is the most appropriate but when i wrote the command an error had occur. It say ?Error in read.table"C:/Users/user/Documents/cfa-1.txt", header = T, sep = "\t",skip=10) :more columns than column names?. Please help me with this as

Estimados por solicitar su ayuda, estoy intentando cambiar el color de una etiqueta de un gráfico, he realizado múltiples intentos sin un resultado satisfactorio. Debido a que necesito realizar múltiples gráficos he realizado una función que dando parámetros de entrada me grafique las variables o los valores que deseo. Mi problema es en la representación de los colores. Los parámetros de la

Hi folks Im currently doin firewall project.. the scenario is like this.. my application server open port number 3079 the server ip is 202.188.0.132. and now the port can be accessed from everywhere. Now i want to block all the everywhere accessed. But my problem is, the application will be accessed by few locations that doing transaction with the application server. and the said locations are

I want to build a robust firewall for a resort installation. The resort''s telephony is entirely VOIP, asterisk based. We have the following internet feeds: 1) 512/512 kb fixed bandwidth leased line with static IP from Telco- primary connection, expensive, to use for VOIP, VPN traffic, mail server, SSH access for remote work. Reliable. 2) 256/512 kb ADSL from Telco, not fixed IP -