R reading multiple files, concatenating results - 


nvar    6957423 rate    1 mac 963.605 maf 0.228126 sing    0 mono    0 titv    1.99326 titv_s  na dp  na qual    na pass    1 filter|pass 1 pass_s  0

i have several files (n=414) format above. in r, read files, transpose, , rbind or concatenate values. files named age_wg2_ind1.vstats, ranging 1 414 (after ind[i].vstats). far, i've tried this: 

txtfiles = list.files(pattern="*.vstats")  (i in 1:length(txtfiles)){      tmp = read.table(txtfiles[i],sep="\t")   ttmp<-t(tmp[i])  colnames(ttmp)<-ttmp[1,];ttmp2<-ttmp[2:nrow(ttmp),] }

error in ttmp[2:nrow(ttmp), ] : subscript out of bounds

1) list files command begin individual #1 , end #414? 2) not sure put [i] retain second row of each file.

thanks!

if files have variable names in first column values in second following should work

l <- lapply(txtfiles , function(i) {                   r <- read.table(i ,sep="\t")                  mat <- t(r[,2])                  colnames(mat) <- r[,1]                  mat                  })  (out <- do.call(rbind , l))

if have (some) different variable names in each file have @ rbind.fill in plyr package

you can @ order of files in txtfiles - numerical order of files not preserved. can pre-process order of txtfiles before lapply loop or files named define file lists 

txtfiles2 <- paste0("age_wg2_ind",1:414,".vstats")

edit

guessing error input error 1 of files - can try this. have made data o show working. if run previous code above (on example data below)you error message 'error in read.table(i, sep = "\t") : no lines available in input'. using trycatch woks.

#some example data  df <- data.frame(letters[1:3] , 1:3) write.table(df,"temp1.out",sep="\t" , row.names=f , col.names=f) write.table(df,"temp2.out",sep="\t", row.names=f , col.names=f) df[,1] <- df[,2] <- null write.table(df,"temp3.out",sep="\t", row.names=f , col.names=f) # 0 columns  #read in data txtfiles <- list.files(pattern="*.out")  l <- lapply(txtfiles , function(i) {                  r <-  trycatch(read.table(i , sep="\t"), error=function(e) null)                  if(!is.null(r)) {                      mat <- t(r[,2])                      colnames(mat) <- r[,1]                      mat         }})  l <- l[!sapply(l, is.null)]  (out <- do.call(rbind , l))

Comments

Post a Comment

Popular posts from this blog

php - SPIP: From Tag directly to an article -

i work spip , plugin called tagsphere works fine tags in spip. have tag groupe put 1 article tag. when click on tag in tagsphere send me before menu can see articles linked tag. want send me directly article without see tag menu before. here code model of thagsphere: <div id="tagsphere-#env{id_article}"> <ul> <boucle_mot(mots){id_groupe ?}> <li>[<a href="#url_mot">(#titre)</a>]</li> </boucle_mot> </ul> </div> anybody idea? if want skip tag page, have link directly article. <b_article> block prevents display tag if no article linked. <div id="tagsphere-#env{id_article}"> <ul> <boucle_mot(mots){id_groupe ?}> <b_article> <li> <a<boucle_article(articles){...
Read more

jquery - isAjaxRequest always return false -

i got error message 404,'model has not been saved' following code my action controller public function actionextend($id) { $model=$this->loadmodel($id); if(yii::app()->request->isajaxrequest) { $model->todate = date('y-m-d h:i:s a',(strtotime('next month',strtotime(date('y-01-d'))))); if($model->save()) { yii::app()->end(); } else { throw new chttpexception(404,'model has not been saved'); } } } the jquery call $("#buttonextend<?php echo $this->post_row;?>").click(function(e){ $.ajax({ type: "post", url: "<?php echo yii::app()->createurl('post/extend', array('id' => $data['id'])); ?>", }); }); why not ajax call ? thank help i found response, missed } , function ...
Read more

ruby on rails - In a controller spec, how to find a specific tag in the generated view? -

i know integration tests preferred need ran in controller test, i'm testing gem injecting html code in view, xhr can't run in feature spec (if can, please explain me how :) ) so rspec controller tests can assert selector present (with capybara) : response.body.should have_selector('#foobar') has_selector? call all method capybara find selector. what want last child of body , assert id in particular. afaik it's not possible have_selector. what : all('body:first-child').first.id.should == '#foobar' however, capybara dsl, defined (more or less): def all(*args) page.all(*args) end and page empty unless use visit it's integrations specs. how can use capybara all method inside rspec controller test ? i can't test right after googling seems trick def page capybara::node::simple.new(response.body) end source
Read more