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 10:28 AM, greg holly <mak.hholly at gmail.com> wrote:
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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______________________________________________ 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.