R help - Feb 2015 - Transform a list of multiple to a data.frame which I want

Dear all:

	I have a list like that,which is a standard str_locate_all() function (stringr
package) output:
$K
   start end
$GSEGTCSCSSK
   start end
[1,]     6   6
[2,]     8   8
$GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK
   start end
[1,]     6   6
$LVECIGQELIFLLPNK
   start end
[1,]     4   4
$NFK
   start end
$HR
   start end
$AYASLFR
   start end

I want to transform this list like that:

ID   start.1  start.2 
K   NA	NA
GSEGTCSCSSK 6 8
GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK 6 NA
LVECIGQELIFLLPNK 4 NA
NFK NA NA
HR NA NA
AYASLFR NA NA

I have already tried to use t() , lapply() but I think it is hard to handle the
NA value and different rows in every matrix

Thanks in advance

Hi Yao,
Messy, but this is the closest I can get:

yhlist<-list(K=matrix(0,ncol=2,nrow=0),
 GSEGTCSCSSK=matrix(c(6,8),nrow=2,ncol=2),
 GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK=matrix(6,ncol=2,nrow=1),
 LVECIGQELIFLLPNK=matrix(6,ncol=2,nrow=1),
 NFK=matrix(0,ncol=2,nrow=0),
 HR=matrix(0,ncol=2,nrow=0),
 AYASLFR=matrix(0,ncol=2,nrow=0))

colnames(yhlist$K)<-c("start","end")
colnames(yhlist$GSEGTCSCSSK)<-c("start","end")
colnames(yhlist$GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK)<-c("start","end")
colnames(yhlist$LVECIGQELIFLLPNK)<-c("start","end")
colnames(yhlist$NFK)<-c("start","end")
colnames(yhlist$HR)<-c("start","end")
colnames(yhlist$AYASLFR)<-c("start","end")


crunch<-function(x) {
 start.1<-ifelse(dim(x)[1],x[1,1],NA)
 start.2<-ifelse(dim(x)[1]>1,x[2,1],NA)
 return(list(start.1,start.2))
}

crunchlist<-sapply(yhlist,crunch,simplify=TRUE)

ID<-colnames(crunchlist)
colnames(crunchlist)<-NULL

data.frame(ID,
 start.1=unlist(crunchlist[1,]),
 start.2=unlist(crunchlist[2,]))

Jim


On Sun, Feb 1, 2015 at 11:53 PM, Yao He <heyao at nibs.ac.cn>
wrote:
> Dear all:
>
>         I have a list like that,which is a standard str_locate_all()
function (stringr package) output:
> $K
>    start end
> $GSEGTCSCSSK
>    start end
> [1,]     6   6
> [2,]     8   8
> $GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK
>    start end
> [1,]     6   6
> $LVECIGQELIFLLPNK
>    start end
> [1,]     4   4
> $NFK
>    start end
> $HR
>    start end
> $AYASLFR
>    start end
>
> I want to transform this list like that:
>
> ID   start.1  start.2
> K   NA  NA
> GSEGTCSCSSK 6 8
> GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK 6 NA
> LVECIGQELIFLLPNK 4 NA
> NFK NA NA
> HR NA NA
> AYASLFR NA NA
>
> I have already tried to use t() , lapply() but I think it is hard to handle
the NA value and different rows in every matrix
>
> Thanks in advance
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.

Does the following work for you.  The only trick is working around the fact
that matrix subscripting does not allow out-of-bounds subscripts but vector
subscripting does.  We do the subscripting in two steps, relying on the
drop=TRUE default in the matrix subscripting operator that converts the
single-
column matrix output to a vector.
> txt <- c("abc", "abcade", "xyz",
"abacad")
> sTxt <- str_locate_all(txt, "a")
> lTxt <- lapply(sTxt, function(st)structure(st[,1][1:2],
names=c("start.1", "start.2")))
> names(lTxt) <- txt
> str(lTxt)
List of 4
 $ abc   : Named int [1:2] 1 NA
  ..- attr(*, "names")= chr [1:2] "start.1"
"start.2"
 $ abcade: Named int [1:2] 1 4
  ..- attr(*, "names")= chr [1:2] "start.1"
"start.2"
 $ xyz   : Named num [1:2] NA NA
  ..- attr(*, "names")= chr [1:2] "start.1"
"start.2"
 $ abacad: Named int [1:2] 1 3
  ..- attr(*, "names")= chr [1:2] "start.1"
"start.2"


Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Sun, Feb 1, 2015 at 4:53 AM, Yao He <heyao at nibs.ac.cn> wrote:
> Dear all:
>
>         I have a list like that,which is a standard str_locate_all()
> function (stringr package) output:
> $K
>    start end
> $GSEGTCSCSSK
>    start end
> [1,]     6   6
> [2,]     8   8
> $GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK
>    start end
> [1,]     6   6
> $LVECIGQELIFLLPNK
>    start end
> [1,]     4   4
> $NFK
>    start end
> $HR
>    start end
> $AYASLFR
>    start end
>
> I want to transform this list like that:
>
> ID   start.1  start.2
> K   NA  NA
> GSEGTCSCSSK 6 8
> GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK 6 NA
> LVECIGQELIFLLPNK 4 NA
> NFK NA NA
> HR NA NA
> AYASLFR NA NA
>
> I have already tried to use t() , lapply() but I think it is hard to
> handle the NA value and different rows in every matrix
>
> Thanks in advance
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
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