two difficult loop

Hi Jim;

I do apologize if bothering. I have run on the real data and here is the
error message I got:

Thanks,

Greg

start  end
Error in regrange[1]:regrange[2] : result would be too long a vector
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf


On Mon, Jun 13, 2016 at 3:19 AM, Jim Lemon <drjimlemon at gmail.com> wrote:

Hi Greg,
Okay, I have a better idea now of what you want. The problem of
multiple matches is still there, but here is a start:

# this data frame actually contains all the values in ref in the "reg"
field
map<-read.table(text="reg p rate
 10276 0.700  3.867e-18
 71608 0.830  4.542e-16
 29220 0.430  1.948e-15
 99542 0.220  1.084e-15
 26441 0.880  9.675e-14
 95082 0.090  7.349e-13
 36169 0.480  9.715e-13
 55572 0.500  9.071e-12
 65255 0.300  1.688e-11
 51960 0.970  1.163e-10
 55652 0.388  3.750e-10
 63933 0.250  9.128e-10
 35170 0.720  7.355e-09
 06491 0.370  1.634e-08
 85508 0.470  1.057e-07
 86666 0.580  7.862e-07
 04758 0.810  9.501e-07
 06169 0.440  1.104e-06
 63933 0.750  2.624e-06
 41838 0.960  8.119e-06
 74806 0.810  9.501e-07
 92643 0.470  1.057e-07
 73732 0.090  7.349e-13
 82451 0.960  8.119e-06
 86042 0.480  9.715e-13
 93502 0.500  9.071e-12
 85508 0.370  1.634e-08
 95082 0.830  4.542e-16",
 header=TRUE)
# same as in your example
ref<-read.table(text="reg1 reg2
 29220     63933
 26441     41838
 06169     10276
 74806     92643
 73732     82451
 86042     93502
 85508     95082",
 header=TRUE)
# sort the "map" data frame
map2<-map[order(map$reg),]
# get a field for the counts
ref$n<-NA
# and a field for the minimum p values
ref$min_p<-NA
# get the number of rows in "ref"
nref<-dim(ref)[1]
for(i in 1:nref) {
 start<-which(map2$reg==ref$reg1[i])
 end<-which(map2$reg==ref$reg2[i])
 cat("start",start,"end",end,"\n")
 # get the range of matches
 regrange<-range(c(start,end))
 # convert this to a sequence spanning all matches
 allreg<-regrange[1]:regrange[2]
 ref$n[i]<-sum(map2$p[allreg] > 0.85)
 ref$min_p[i]<-min(map2$p[allreg])
}

This example uses the span from the first match of "reg1" to the last
match of "reg2". This may not be what you want, so let me know if
there are further constraints.

Jim

On Mon, Jun 13, 2016 at 12:35 PM, greg holly <mak.hholly at gmail.com>
wrote:

Hi Bert;

I do appreciate for this. I need check your codes on task2 tomorrow at

my

office on the real data as I have difficulty (because a technical

issue) to

remote connection. I am sure it will work well.

I am sorry that I was not able to explain my first question. Basically

Values in ref data represent the region of chromosome. I need choose

these

regions in map (all regions values in ref data are exist in map data in

the

first column -column map$reg). And then summing up the column "map$rate

and

count the numbers that gives >0.85. For example, consider  the first

row in

data ref. They are 29220   and  63933. After sorting the first column in
map then summing column "map$rate" only between 29220   to  63933 in

sorted

map and cut off at >0.85. Then count how many rows in sorted map gives

0.85. For example consider there are 38 rows between 29220   in  63933

in sorted

map$reg and only summing first 12 of them  gives>0.85. Then my answer is
going to be 12 for 29220   -  63933 in ref.

Thanks I lot for your patience.

Cheers,
Greg

On Sun, Jun 12, 2016 at 10:35 PM, greg holly <mak.hholly at gmail.com>

wrote:

Hi Bert;

I do appreciate for this. I need check your codes on task2 tomorrow at

my

office on the real data as I have difficulty (because a technical

issue) to

remote connection. I am sure it will work well.

I am sorry that I was not able to explain my first question. Basically

Values in ref data represent the region of chromosome. I need choose

these

regions in map (all regions values in ref data are exist in map data

in the

first column -column map$reg). And then summing up the column

"map$rate and

count the numbers that gives >0.85. For example, consider  the first

row in

data ref. They are 29220   and  63933. After sorting the first column

in

map then summing column "map$rate" only between 29220   to  63933 in
sorted map and cut off at >0.85. Then count how many rows in sorted map
gives >0.85. For example consider there are 38 rows between 29220   in
 63933 in sorted map$reg and only summing first 12 of them  gives>0.85.
Then my answer is going to be 12 for 29220   -  63933 in ref.

Thanks I lot for your patience.

Cheers,
Greg

On Sun, Jun 12, 2016 at 6:36 PM, Bert Gunter <bgunter.4567 at gmail.com>
wrote:

Greg:

I was not able to understand your task 1. Perhaps others can.

My understanding of your task 2 is that for each row of ref, you wish
to find all rows,of map such that the reg values in those rows fall
between the reg1 and reg2 values in ref (inclusive change <= to < if
you don't want the endpoints), and then you want the minimum map$p
values of all those rows. If that is correct, I believe this will do
it (but caution, untested, as you failed to provide data in a
convenient form, e.g. using dput() )

task2 <- with(map,vapply(seq_len(nrow(ref)),function(i)
min(p[ref[i,1]<=reg & reg <= ref[i,2] ]),0))


If my understanding is incorrect, please ignore both the above and the
following:


The "solution" I have given above seems inefficient, so others may be
able to significantly improve it if you find that it takes too long.
OTOH, my understanding of your specification is that you need to
search for all rows in map data frame that meet the criterion for each
row of ref, and without further information, I don't know how to do
this without just repeating the search 560 times.


Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sun, Jun 12, 2016 at 1:14 PM, greg holly <mak.hholly at gmail.com>

wrote:

Dear all;



I have two data sets, data=map and data=ref). A small part of each

data

set

are given below. Data map has more than 27 million and data ref has

about

560 rows. Basically I need run two different task. My R codes for

these

task are given below but they do not work properly.

I sincerely do appreciate your helps.


Regards,

Greg



Task 1)

For example, the first and second columns for row 1 in data ref are

29220

63933. So I need write an R code normally first look the first row

in

ref

(which they are 29220 and 63933) than summing the column of

"map$rate"

and

give the number of rows that >0.85. Then do the same for the second,
third....in ref. At the end I would like a table gave below (the

results I

need). Please notice the all value specified in ref data file are

exist

in

map$reg column.



Task2)

Again example, the first and second columns for row 1 in data ref

are

29220

63933. So I need write an R code give the minimum map$p for the

29220

-63933 intervals in map file. Than

do the same for the second, third....in ref.




#my attempt for the first question

temp<-map[order(map$reg, map$p),]

count<-1

temp<-unique(temp$reg

for(i in 1:length(ref) {

  for(j in 1:length(ref)

  {

temp1<-if (temp[pos[i]==ref[ref$reg1,] &

(temp[pos[j]==ref[ref$reg2,]

& temp[cumsum(temp$rate)

0.70,])

count=count+1

    }

}

#my attempt for the second question



temp<-map[order(map$reg, map$p),]

count<-1

temp<-unique(temp$reg

for(i in 1:length(ref) {

  for(j in 1:length(ref)

  {

temp2<-if (temp[pos[i]==ref[ref$reg1,] &

(temp[pos[j]==ref[ref$reg2,])

output<-temp2[temp2$p==min(temp2$p),]

    }

}



Data sets


  Data= map

  reg   p      rate

 10276 0.700  3.867e-18

 71608 0.830  4.542e-16

 29220 0.430  1.948e-15

 99542 0.220  1.084e-15

 26441 0.880  9.675e-14

 95082 0.090  7.349e-13

 36169 0.480  9.715e-13

 55572 0.500  9.071e-12

 65255 0.300  1.688e-11

 51960 0.970  1.163e-10

 55652 0.388  3.750e-10

 63933 0.250  9.128e-10

 35170 0.720  7.355e-09

 06491 0.370  1.634e-08

 85508 0.470  1.057e-07

 86666 0.580  7.862e-07

 04758 0.810  9.501e-07

 06169 0.440  1.104e-06

 63933 0.750  2.624e-06

 41838 0.960  8.119e-06


 data=ref

  reg1         reg2

  29220     63933

  26441     41838

  06169     10276

  74806     92643

  73732     82451

  86042     93502

  85508     95082



       the results I need

     reg1      reg2 n

   29220   63933  12

   26441   41838   78

   06169 10276  125

   74806 92643   11

   73732 82451   47

   86042 93502   98

   85508 95082  219

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