hi I have a huge counts file containing tags and all the related samples (129 samples) and I want to load only some columns(samples) to DGEList object not the result(counts) of all samples. I have used scan but it does not work. Thanks alot Best Regards -- output of sessionInfo(): > scan ("count.txt", what = list (0,NULL,0),skip=2,flush=TRUE) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got 'ENSG00000000005' ############################# d <- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("null",126)),header=TRUE) Error in methods::as(data[[i]], colClasses[i]) : no method or default for coercing "character" to "null" > d <- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("NA",126)),header=TRUE) Error in methods::as(data[[i]], colClasses[i]) : no method or default for coercing "character" to "NA" -- Sent via the guest posting facility at bioconductor.org.

On 04/12/2012 03:05 AM, narges [guest] wrote: > > hi > I have a huge counts file containing tags and all the related samples (129 samples) and I want to load only some columns(samples) to DGEList object not the result(counts) of all samples. > I have used scan but it does not work. > Thanks alot > Best Regards > > > -- output of sessionInfo(): > >> scan ("count.txt", what = list (0,NULL,0),skip=2,flush=TRUE) > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > scan() expected 'a real', got 'ENSG00000000005' > ############################# If you had a text file with a character column, then 1000 numeric columns, and you wanted to read the character column and the 2nd, 10th and 100th numeric columns you might say reals <- rep(list(NULL), 1000) reals[c(2, 10, 100)] <- list(numeric()) what <- c(list(character()), reals) you'd then end up with something like > head(what) [[1]] character(0) [[2]] NULL [[3]] numeric(0) [[4]] NULL [[5]] NULL [[6]] NULL and these would be used in the 'what' argument to scan. An additional 'trick' is to name the elements of 'what'; these are then included as the names of the elements returned by scan. > d<- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("null",126)),header=TRUE) > Error in methods::as(data[[i]], colClasses[i]) : > no method or default for coercing "character" to "null" "NULL" rather than "null", so along the lines of reals <- rep("NULL", 1000) reals[c(2, 10, 100)] <- "numeric" colClasses <- c("character", reals) and > head(colClasses) [1] "character" "NULL" "numeric" "NULL" "NULL" "NULL" Martin >> d<- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("NA",126)),header=TRUE) > Error in methods::as(data[[i]], colClasses[i]) : > no method or default for coercing "character" to "NA" > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793