R help - Feb 2014 - Form groups of lines and select specific values

Hi,

Not sure I understand it correctly.
May be this helps:

dat <- read.table(text="type1????? chrx???????? startx?????????
endx????????? chry?????????? starty????? endy???????? type2
gain_765?? chr15???? 9681969?????? 9685418????? chr15??????? 9660912???
9712719??? loss_1136
gain_766?? chr15???? 9706682?????? 9852347????? chr15??????? 9660912???
9712719??? loss_1136
gain_766?? chr15???? 9706682?????? 9852347????? chr15??????? 9765125???
9863990??? loss_765
gain_780?? chr20???? 9706682?????? 9852347????? ch20???????? 9765125???
9863990??? loss_769
gain_760?? chr15???? 9706682?????? 9852347????? chr15??????? 9660912???
9712719??? loss_1137
gain_760?? chr15???? 9706682?????? 9852347????? chr15??????? 9765125???
9863990??? loss_763",sep="",header=TRUE,stringsAsFactors=FALSE)
?indx <- rle(dat$chry)$lengths
?indx1 <- cumsum(indx)
?indx2 <- indx1-(indx-1)
chr <- dat$chrx[indx1]
start <-
do.call(pmin,data.frame(startx=dat$startx[indx2],starty=dat$starty[indx2]))
end <- do.call(pmax,data.frame(endx=dat$endx[indx1],endy=dat$endy[indx1]))
dat2 <- data.frame(chr,start,end,stringsAsFactors=FALSE)

dat2
#??? chr?? start???? end
#1 chr15 9660912 9863990
#2 chr20 9706682 9863990
#3 chr15 9660912 9863990
A.K.



I would like to form group of lines based in interconection (two ways) 
between "type1" collumn and "type2" collumn. The logic is:
if a string
in "type1" are in the same line of "type2" collumn they are
in the same
group. However if "type2" are more than one line all those are in the 
same group. 

Please take a look in the first 3 lines: "gain_765" and 
"loss_1136" are related. However, "loss_1136" are related
with
"gain_766" and subsenquently "gain_766" are relate with
"loss_765". Then
 these is my group: 1- "gain_765", 2- "loss_1136",
3-"gain_766",
4-"loss_765". 

Inside this group I wanna to make a new line with string in 
"chrx" on first line of the group; lowest value in "startx"
and
"starty"; larger value in "endx" and "endy".
Follow a example of my
data: 

?type1 ? ? ?chrx ? ? ? ? startx ? ? ? ? ?endx ? ? ? ? ?chry ? ? ? ? ? starty ? ?
?endy ? ? ? ? type2
gain_765 ? chr15 ? ? 9681969 ? ? ? 9685418 ? ? ?chr15 ? ? ? ?9660912 ? ?9712719
? ?loss_1136
gain_766 ? chr15 ? ? 9706682 ? ? ? 9852347 ? ? ?chr15 ? ? ? ?9660912 ? ?9712719
? ?loss_1136
gain_766 ? chr15 ? ? 9706682 ? ? ? 9852347 ? ? ?chr15 ? ? ? ?9765125 ? ?9863990
? ?loss_765
gain_780 ? chr20 ? ? 9706682 ? ? ? 9852347 ? ? ?ch20 ? ? ? ? 9765125 ? ?9863990
? ?loss_769
gain_760 ? chr15 ? ? 9706682 ? ? ? 9852347 ? ? ?chr15 ? ? ? ?9660912 ? ?9712719
? ?loss_1137
gain_760 ? chr15 ? ? 9706682 ? ? ? 9852347 ? ? ?chr15 ? ? ? ?9765125 ? ?9863990
? ?loss_763

To first group (line 1 to 3) this is the expected output: 

? ? ?chr ? ? ? start ? ? ? ?end 
? ?chr15 ? ?9660912 ? 9863990 

Now, please take a look in line 4: "gain_780" is related just 
with "loss_769". Is this group (just line 4) the output expected 
follows: 

? ? ?chr ? ? ? ? start ? ? ? ?end 
? ? chr20 ? ? 9706682 ? 9863990 

Now, lines 5 and 6 the group is formed by "gain_760";
"loss_1137" and "loss_763". In this last case the expected
output is:

? ? ?chr ? ? ? ? start ? ? ? ? end 
? ? chr15 ? ? 9660912 ? 9863990 

But, I have many of this cases in thousands of lines. Therefore, I need all
results in a unique output, like that:

? ? ? chr ? ? ? start ? ? ? ? end 
? ? ?chr15 ? ?9660912 ? 9863990 
? ? ?chr20 ? ?9706682 ? 9863990 
? ? ?chr15 ? ?9660912 ? 9863990 

Cheers.