Dear Jim,
2013/8/5 jim holtman <jholt...@gmail.com>: > Couple of things to try. May have an extra quote, so put: > > quote = '' thank you very much. That did the trick. Much obliged! > > as one of the parameters. Also, might have comments, so try: > > comment.char = "" > > Take alook at your file and determine what line was the last complete one > and see if there might be a problem in that line, or preceeding ones. > > On Mon, Aug 5, 2013 at 7:11 AM, Asis Hallab <asis.hal...@gmail.com> wrote: >> >> Dear R experts, >> >> I have a large table saved in a file called "plant_genome.gff". The >> file has 481848 lines in nine columns, which are TAB delimited, and is >> 53 MegaBytes large. >> For anyone who might know the GFF3 format: The table holds a plant >> genome's annotation. >> >> If I read in the table with >> read.table( "plant_genome.gff" ) >> I get the following error >> "line 2 did not have 12 elements". >> >> If I read in the table with >> read.table( "plant_genome.gff", sep="\t" ) >> no error or warning is given, but my resulting table has only 193547 >> instead of the expected 481848 rows! 60% of the lines are omitted. >> >> Also passing in the arguments >> as.is = TRUE >> or setting the columns' classes with >> colClasses = c( "character", …, "integer", "integer", "numeric", >> "character", … ) >> # columns 4, and 5 are integers, column 6 is numeric, all others >> are characters >> does not resolve the problem. >> >> If I read in the file with readLines and then manually split them using >> strplit(…) >> and combine them into a data.frame with >> as.data.frame( do.call( "rbind", splitted.lines ), colClasses=…) >> I get the expected and correct data.frame, representing my GFF3 data. >> >> My questions are: >> 1) Am I using read.table wrong, or did I miss something in the >> documentation? >> 2) Or is this is known problem with large TAB delimited tables, whose >> columns contain white-spaces and are not surrounded by quotes? >> >> Unfortunately due to the unpublished nature of the plant genome I am >> not allowed to give access to the GFF table that causes this problem. >> >> Any ideas, hints, help - or comments on my stupidity having missed >> something important - will be much appreciated! >> >> Cheers! >> ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
