Hi Jeff an many thank's for your time. I meant that it was easy as in not requiring som many steps...
I have managed to get it to run and it has solved my problem perfectly. Thank you for all your tips and instructions! Up until now, I have used excel for all problems similar to this one and only used R for the statistics part. I intend to make a permanent swith to R as I can see the benefits. I am just severely frustrated by my own inabilities. Therefore, once again many thank´s for your time! kind regards Anna ><((((º>`•. . • `•. .• `•. . ><((((º>`•. . • `•. .• `•. .><((((º>`•. . • `•. .• >`•. .><((((º> Anna Zakrisson Braeunlich PhD student Department of Ecology, Environment and Plant Sciences Stockholm University Svante Arrheniusv. 21A SE-106 91 Stockholm Sweden/Sverige Lives in Berlin. For paper mail: Katzbachstr. 21 D-10965, Berlin Germany/Deutschland E-mail: anna.zakris...@su.se Tel work: +49-(0)3091541281 Mobile: +49-(0)15777374888 LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b ><((((º>`•. . • `•. .• `•. . ><((((º>`•. . • `•. .• `•. .><((((º>`•. . • `•. .• >`•. .><((((º> ________________________________________ From: Jeff Newmiller [jdnew...@dcn.davis.ca.us] Sent: 19 October 2014 08:25 To: Anna Zakrisson Braeunlich Cc: Ista Zahn; r-help@r-project.org Subject: Re: [R] seqinr ?: Splitting a factor name into several columns. Dealing with metabarcoding data. On Sat, 18 Oct 2014, Anna Zakrisson Braeunlich wrote: > Thank you! That was a easy and fast solution! If it was so easy, why couldn't you adapt Ista's solution? I suspect it is because you don't understand his suggestion. > May I post a follow-up question? (I am not sure if this would rather > should be posted as a new question, but I post it here and then I can > re-post it if this is the wrong place to ask this). I am ever so > grateful for your help! This probably should have been a new thread, but I will bite anyway. > /Anna > > > ######################### FOLLOW-UP QUESTION > #################################### > > df1 <- data.frame(cbind(Identifier = c("M123.B23.VJHJ", "M123.B24.VJHJ", > "M123.B23.VLKE", "M123.B23.HKJH", > "M123.B24.LKJH"), > Sequence = c("ATATATATATA", > "ATATATATATA", > "ATATAGCATATA", > "ATATATAGGGTA", > "ATCGCGCGAATA"))) Just because R has a habit of making factors at the drop of a hat doesn't mean that if your data are still not ready to be treated as factors that you have to accept what it does. When you read the data in via read.csv you can use the colClasses argument or the stringsAsFactors argument to stop that. You can use stringsAsFactors when you create the data frame also, and you can always go back and turn any particular column into a factor after you are done manipulating characters. Also, somewhere you picked up the bad habit of using cbind before you make your data frame... that is almost never a good idea, because in data frames each column can be have its own storage mode, while cbind creates a matrix where every element must have the same storage mode. df1 <- data.frame( Identifier = c( "M123.B23.VJHJ", "M123.B24.VJHJ" , "M123.B23.VLKE", "M123.B23.HKJH" , "M123.B24.LKJH" ) , Sequence = c( "ATATATATATA", "ATATATATATA" , "ATATAGCATATA", "ATATATAGGGTA" , "ATCGCGCGAATA" ) , stringsAsFactors=FALSE ) > > # as a follow-up question: > # How can I split the identifier in df1 above into several columns based on > the > # separating dots? The real data includes thousands of rows. > # This is what I want it to look like in the end: > > df1_solution <- data.frame(cbind(Identifier1 = c("M123", "M123", > "M123", "M123", > "M123"), > Identifier2 = c("B23", "B24", "B23", "B23", "B24"), > Identifier3 = c("VJHJ", "VJHJ", "VLKE", "HKJH", > "LKJH"), > Sequence = c("ATATATATATA", "ATATATATATA", > "ATATAGCATATA", "ATATATAGGGTA", > "ATCGCGCGAATA"))) df1_solution <- data.frame( Identifier1 = c( "M123", "M123" , "M123", "M123" , "M123" ) , Identifier2 = c( "B23", "B24", "B23" , "B23", "B24" ) , Identifier3 = c( "VJHJ", "VJHJ" , "VLKE", "HKJH", "LKJH") , Sequence = c( "ATATATATATA", "ATATATATATA" , "ATATAGCATATA", "ATATATAGGGTA" , "ATCGCGCGAATA" ) , stringsAsFactors=FALSE ) > # I am very grateful for your help! I am no whiz at R and everything I know > # is self-taught. Therefore, some basics can turn out to be quite some > # obsatcles for me. > # /Anna Pretty much all of us are here to teach ourselves R, Anna. Keep reading other people's questions. Learn to try each fragment alone at the command line to figure out what is happening. Use the str() function frequently. # the basic split parts <- strsplit( as.character( df1$Identifier ), ".", fixed=TRUE ) # extension of Ista's approach to assembly ans1 <- data.frame( Identifier1 = rep( NA, nrow( ans1 ) ) , Identifier2 = rep( NA, nrow( ans1 ) ) , Identifier3 = rep( NA, nrow( ans1 ) ) , stringsAsFactors = FALSE ) # note all memory is pre-allocated above... avoid successively # accumulating rows with rbind... that would be very slow for ( rw in seq_along( df1$Identifier ) ) { v <- parts[[ rw ]] ans1[ rw, "Identifier1" ] <- v[ 1 ] ans1[ rw, "Identifier2" ] <- v[ 2 ] ans1[ rw, "Identifier3" ] <- v[ 3 ] } ans1$Sequence <- df1$Sequence #---- alternative method of assembly # uses "list-to-data.frame apply" from plyr package library(plyr) ans2 <- ldply( parts , function( v ) { # called once for each item in parts list # all single-row data frames created in this # function are concatenated at once by ldply to # make one big data.frame "ans2" data.frame( Identifier1=v[1] , Identifier2=v[2] , Identifier3=v[3] , stringsAsFactors=FALSE ) } ) ans2$Sequence <- DF$Sequence >> <((((?>`?. . ? `?. .? `?. . ><((((?>`?. . ? `?. .? `?. .><((((?>`?. . ? `?. >> .? `?. .><((((?> > > Anna Zakrisson Braeunlich > PhD student > > Department of Ecology, Environment and Plant Sciences > Stockholm University > Svante Arrheniusv. 21A > SE-106 91 Stockholm > Sweden/Sverige > > Lives in Berlin. > For paper mail: > Katzbachstr. 21 > D-10965, Berlin > Germany/Deutschland > > E-mail: anna.zakris...@su.se > Tel work: +49-(0)3091541281 > Mobile: +49-(0)15777374888 > LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b > >> <((((?>`?. . ? `?. .? `?. . ><((((?>`?. . ? `?. .? `?. .><((((?>`?. . ? `?. >> .? `?. .><((((?> > > ________________________________________ > From: Ista Zahn [istaz...@gmail.com] > Sent: 13 October 2014 15:42 > To: Anna Zakrisson Braeunlich > Cc: r-help@r-project.org > Subject: Re: [R] seqinr ?: Splitting a factor name into several columns. > Dealing with metabarcoding data. > > Hi Anna, > > > On Sun, Oct 12, 2014 at 3:24 AM, Anna Zakrisson Braeunlich > <anna.zakris...@su.se> wrote: >> Hi, >> >> I have a question how to split a factor name into different columns. I have >> metabarcoding data and need to merge the FASTA-file with the taxonomy- and >> counttable files (dataframes). To be able to do this merge, I need to >> isolate the common identifier, that unfortunately is baked in with a lot of >> other labels in the factor name eg: >> sequence identifier: >> M01271_77_000000000.A8J0P_1_1101_10150_1525.1.322519.sample_1.sample_2 >> >> I want to split this name at every "." to get several columns: >> column1: M01271_77_000000000 >> column2: A8J0P_1_1101_10150_1525 >> column3: 1 >> column4: 322519 >> column5: sample_1 >> column6: sample_2 >> >> I must add that I have no influence on how these names are given. This is >> how thay are supplied from Illumina Miseq. I just need to be able to deal >> with it. >> >> Here is some extremely simplified dummy data to further show the issue at >> hand: >> >> df1 <- data.frame(cbind(X = 1:10, Y = rnorm(10)), >> Z.identifierA.B1298712 = factor(rep(LETTERS[1:2], each = >> 5))) >> df2 <- data.frame(cbind(B = 13:22, K = rnorm(10)), >> Q.identifierA.B4668726 = factor(rep(LETTERS[1:2], each = >> 5))) >> >> # I have metabarcoding data with one FASTA-file, one count table and one >> taxonomy file >> # Above dummy data is just showing the issue at hand. I want to be able to >> merge my three >> # original data frames (here, the dummy data is only two dataframes). The >> problem is that >> # the only identifier that is commmon for the dataframes is "hidden" in the >> # factor name eg: Z.identifierA.1298712 and Q.identifierA.4668726. I hence >> need to be able >> # to split this name up into different columns to get "identifierA" alone as >> one column name >> # Then I can merge the dataframes. >> # How can I do this in R. I know that it can be done in excel, but I would >> like to >> # produce a complete R-script to get a fast pipeline and avoid copy and >> paste errors. >> # This is what I want it to look: >> >> df1.goal <- data.frame(cbind(X = 1:10, Y = rnorm(10)), >> Z = factor(rep(LETTERS[1:2], each = 5)), >> identifierA = factor(rep(LETTERS[1:2], each = 5)), >> B1298712 = factor(rep(LETTERS[1:2], each = 5))) > > Use strsplit to separate the components, something like > > separateNames <- strsplit(names(df1)[3], split = "\\.")[[1]] > for(name in separateNames) { > df1[[name]] <- df1[[3]] > } > df1[[3]] <- NULL > > Best, > Ista > >> >> # Many thank's and with kind regards >> Anna Zakrisson >> >>> <((((?>`?. . ? `?. .? `?. . ><((((?>`?. . ? `?. .? `?. .><((((?>`?. . ? `?. >>> .? `?. .><((((?> >> >> Anna Zakrisson Braeunlich >> PhD student >> >> Department of Ecology, Environment and Plant Sciences >> Stockholm University >> Svante Arrheniusv. 21A >> SE-106 91 Stockholm >> Sweden/Sverige >> >> Lives in Berlin. >> For paper mail: >> Katzbachstr. 21 >> D-10965, Berlin >> Germany/Deutschland >> >> E-mail: anna.zakris...@su.se >> Tel work: +49-(0)3091541281 >> Mobile: +49-(0)15777374888 >> LinkedIn: http://se.linkedin.com/pub/anna-zakrisson-braeunlich/33/5a2/51b >> >>> <((((?>`?. . ? `?. .? `?. . ><((((?>`?. . ? `?. .? `?. .><((((?>`?. . ? `?. >>> .? `?. .><((((?> >> >> [[alternative HTML version deleted]] >> >> >> ______________________________________________ >> 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. >> > > ______________________________________________ > 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. > --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- ______________________________________________ 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.
