Hi Arun, Many thanks for following this through. Based on your earlier suggestion with CEBPA, I also edited the code and now it seems work (I removed the non exiting names). I looked into the current code that you have sent below and I learnt a few more things. So thank you again. Your skills in R is very good. Could you suggest some resources for advance R programming. I am fairly comfortable with R, but need to keep abreast with the latest R libraries that can make life a lot simpler. Thanks again, -M On Fri, Jul 26, 2013 at 2:20 PM, arun kirshna [via R] < ml-node+s789695n4672460h72@n4.nabble.com> wrote: > Hi, > Using the example code without removing CEBPA: > gset<- read.table("Names.txt",header=TRUE,stringsAsFactors=FALSE) > temp1<- read.table("Data.txt",header=TRUE,stringsAsFactors=FALSE) > lst1<-split(temp1,temp1$Names) > mat1<-combn(gset[,1],2) > library(plyr) > lst2<-lapply(split(mat1,col(mat1)),function(x){lst1[x][all(lapply(lst1[x],length)==2)]}) > > lst3<-lapply(lst2[lapply(lst2,length)==2],function(x) {x1<- > join_all(x,by="patient_id",type="inner");x2<-x1["patient_id"];row.names(x2)<-if(nrow(x1)!=0) > paste(x1[,1],x1[,3],1:nrow(x1),sep="_") else NULL;x2 }) > Reduce(rbind,lst3) > # patient_id > #DNMT3A_FLT3_1 LAML-AB-2811-TB > #DNMT3A_FLT3_2 LAML-AB-2816-TB > #DNMT3A_FLT3_3 LAML-AB-2818-TB > #DNMT3A_IDH1_1 LAML-AB-2802-TB > #DNMT3A_IDH1_2 LAML-AB-2822-TB > #DNMT3A_NPM1_1 LAML-AB-2802-TB > #DNMT3A_NPM1_2 LAML-AB-2809-TB > #DNMT3A_NPM1_3 LAML-AB-2811-TB > #DNMT3A_NPM1_4 LAML-AB-2816-TB > #DNMT3A_NRAS_1 LAML-AB-2816-TB > #FLT3_NPM1_1 LAML-AB-2811-TB > #FLT3_NPM1_2 LAML-AB-2812-TB > #FLT3_NPM1_3 LAML-AB-2816-TB > #FLT3_NRAS_1 LAML-AB-2816-TB > #IDH1_NPM1_1 LAML-AB-2802-TB > #NPM1_NRAS_1 LAML-AB-2816-TB > > > > > ########From your original dataset: > gset<- read.table("SampleGenes.txt",header=TRUE,stringsAsFactors=FALSE) > temp0<- > read.table("LAML-TB.final_analysis_set.txt",header=TRUE,stringsAsFactors=FALSE,sep="\t") > > temp1<- temp0[,c("Hugo_Symbol","firehose_patient_id")] > str(temp1) > #'data.frame': 2221 obs. of 2 variables: > # $ Hugo_Symbol : chr "TBX15" "TCHHL1" "DNMT3A" "IDH1" ... > # $ firehose_patient_id: chr "LAML-AB-2802-TB" "LAML-AB-2802-TB" > "LAML-AB-2802-TB" "LAML-AB-2802-TB" ... > lst1<-split(temp1,temp1$Hugo_Symbol) > length(lst1) > #[1] 1607 > mat1<-combn(gset[,1],2) # Generate all > lst2<-lapply(split(mat1,col(mat1)),function(x){lst1[x][all(lapply(lst1[x],length)==2)]}) > > length(lst2) > #[1] 105 > > > lst3<-lapply(lst2[lapply(lst2,length)==2],function(x) {x1<- > join_all(x,by="firehose_patient_id",type="inner");x2<-x1["firehose_patient_id"];row.names(x2)<-if(nrow(x1)!=0) > paste(x1[,1],x1[,3],1:nrow(x1),sep="_") else NULL;x2 }) > res<-Reduce(rbind,lst3) > nrow(res) > #[1] 234 > head(res) > # firehose_patient_id > #NPM1_FLT3_1 LAML-AB-2811-TB > #NPM1_FLT3_2 LAML-AB-2812-TB > #NPM1_FLT3_3 LAML-AB-2816-TB > #NPM1_FLT3_4 LAML-AB-2818-TB > #NPM1_FLT3_5 LAML-AB-2825-TB > #NPM1_FLT3_6 LAML-AB-2836-TB > > > > > Regarding your second question: > setdiff(gset[,1],unique(temp1[,1])) # CEBPA was not found in the temp1[,1] > #[1] "CEBPA" > mat2<- combn(gset[-5,1],2) > vec1<- apply(mat2,2,paste,collapse="_") > vec2<-unique(gsub("(.*\\_.*)\\_.*","\\1",row.names(res))) > setdiff(vec1,vec2) > #[1] "NPM1_TP53" "NPM1_EZH2" "NPM1_RUNX1" "NPM1_ASXL1" "NPM1_KDM6A" > #[6] "FLT3_TP53" "FLT3_EZH2" "FLT3_KRAS" "FLT3_ASXL1" "FLT3_KDM6A" > #[11] "IDH1_TP53" "IDH1_KRAS" "NRAS_IDH2" "NRAS_KRAS" "NRAS_ASXL1" > #[16] "NRAS_KDM6A" "TP53_EZH2" "TP53_IDH2" "TP53_RUNX1" "TP53_KRAS" > #[21] "TP53_WT1" "TP53_ASXL1" "TP53_KDM6A" "EZH2_IDH2" "EZH2_WT1" > #[26] "EZH2_ASXL1" "EZH2_KDM6A" "IDH2_TET2" "IDH2_KDM6A" > "RUNX1_KDM6A" > #[31] "KRAS_WT1" "KRAS_KDM6A" "WT1_ASXL1" "WT1_TET2" "WT1_KDM6A" > #[36] "ASXL1_TET2" "ASXL1_KDM6A" "TET2_KDM6A" > A.K. > > > ----- Original Message ----- > From: arun <[hidden email]> > > To: Manisha <[hidden email]> > > Cc: R help <[hidden email]> > > Sent: Friday, July 26, 2013 11:18 AM > Subject: Re: Pairwise comparison between columns, logic > > Hi Manisha, > I didn't run your dataset as I am on the way to college. But, from the > error reported, I think it will be due to some missing combinations in one > of the dataset. For ex. if you run my previous code without removing > CEBPA: > ie. > mat1<- combn(gset[,1],2) > > > lst2<-lapply(split(mat1,col(mat1)),function(x) > {x1<-join_all(lst1[x],by="patient_id",type="inner");x1["patient_id"] } ) > #Error: All inputs to rbind.fill must be data.frames > > > So, check whether all the combinations are available in the `lst1`. > > 2. I will get back to you once I run it. > A.K. > > > > > > ________________________________ > From: Manisha <[hidden email]> > > To: arun <[hidden email]> > > Sent: Friday, July 26, 2013 11:09 AM > Subject: Re: Pairwise comparison between columns, logic > > > > Hi Arun, > I ran the script on a larger dataset and I seem to be running into this > following error: > Error: All inputs to rbind.fill must be data.frames > after the step; > lst2<-lapply(split(mat1,col(mat1)),function(x) > {x1<-join_all(lst1[x],by="firehose_patient_id",type="inner");x1["firehose_patient_id"]}) > > I tried a few things to solve the issue but I am not able to. The format > of input files and data are same as in the code you posted. > Could you suggest me something? > I have attached my input files on which I am trying to run the code. See > attached code as well. Minor changes have been made by me. > > 2. I have another question. From your code how do also capture those pairs > of names that donot have any common patient id? > > Thanks again, > -M > > > On Fri, Jul 26, 2013 at 9:29 AM, arun <[hidden email]> > wrote: > > Hi M, > > >No problem. > >Regards, > >Arun > > > > > > > > > >----- Original Message ----- > >From: "[hidden email]" > <[hidden email] > > >To: [hidden email] > >Cc: > >Sent: Friday, July 26, 2013 9:27 AM > >Subject: Re: Pairwise comparison between columns, logic > > > >Thanks for the code. It is elegant and does what I need. Learnt some new > things. > >-M > > > > > >_____________________________________ > >Sent from http://r.789695.n4.nabble.com > > > > ______________________________________________ > [hidden email] 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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Pairwise-comparison-between-columns-logic-tp4672356p4672460.html > To unsubscribe from Pairwise comparison between columns, logic, click > here > . > NAML > -- View this message in context: http://r.789695.n4.nabble.com/Pairwise-comparison-between-columns-logic-tp4672356p4672461.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]]