Re: [R] Merge the data from multiple text files
Thank you David Winsemius and David L Carlson.
@David L Carlson, Thank you for the code. I have one more issue, while merging
the files. Please advice.For example
In text file 1:
A = not(B or C)B = A and CC = D
In text file 2:
A = not(C or D) and (D and E)
So when I merge using your code, it merges A = not(B or C) and (D and E). How
do I merge A as A= not(B or C or D) and (D and E) ? I also have duplicates
like A= not(B or C) and not (C or D) instead as A= not(B or C or D) ThanksPriya
On Sunday, 6 January 2019 4:39 AM, David L Carlson
wrote:
To expand on David W's answer, here is an approach to your example. If you
have many text files, you would want to process them together rather than
individually. You gave us two examples so I'll use those and read them from the
console using readLines(), but you would use the same function to open the
files on your computer:
> TF1 <- readLines(n=3)
A = not(B or C)
B = A and C
C = D
>
> TF2 <- readLines(n=2)
A = D and E
B = not(D)
>
> TF <- sort(c(TF1, TF2))
> TF
[1] "A = D and E" "A = not(B or C)" "B = A and C" "B = not(D)"
[5] "C = D"
Now we have combined the files into a single character vector called TF and
sorted them. Next we need to parse them into the left and right hand sides. We
will replace " = " with "\t" (tab) to do that:
> TF.delim <- gsub(" = ", "\t", TF)
> TF.data <- read.delim(text=TF.delim, header=FALSE, as.is=TRUE)
> colnames(TF.data) <- c("LHS", "RHS")
> print(TF.data, right=FALSE)
LHS RHS
1 A D and E
2 A not(B or C)
3 B A and C
4 B not(D)
5 C D
TF.data is a data frame with two columns. The tricky part is to add surrounding
parentheses to rows 1 and 3 to get your example output:
> paren1 <- grepl("and", TF.data$RHS)
> paren2 <- !grepl("\\(*\\)", TF.data$RHS)
> paren <- apply(cbind(paren1, paren2), 1, all)
> TF.data$RHS[paren] <- paste0("(", TF.data$RHS[paren], ")")
> print(TF.data, right=FALSE)
LHS RHS
1 A (D and E)
2 A not(B or C)
3 B (A and C)
4 B not(D)
5 C D
The first three lines identify the rows that have the word "and" but do not
already have parentheses. The fourth line adds the surrounding parentheses.
Finally we will combine the rows that belong to the same LHS value with split
and create a list:
> TF.list <- split(TF.data$RHS, TF.data$LHS)
> TF.list
$`A`
[1] "(D and E)" "not(B or C)"
$B
[1] "(A and C)" "not(D)"
$C
[1] "D"
> TF.and <- lapply(TF.list, paste, collapse=" and ")
> TF.final <- lapply(names(TF.and), function(x) paste(x, "=", TF.and[[x]]))
> TF.final <- do.call(rbind, TF.final)
> TF.final
[,1]
[1,] "A = (D and E) and not(B or C)"
[2,] "B = (A and C) and not(D)"
[3,] "C = D"
> write(TF.final, file="TF.output.txt")
The text file "TF.output.txt" contains the three lines.
--
David L. Carlson
Department of Anthropology
Texas A&M University
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius
Sent: Saturday, January 5, 2019 1:12 PM
Subject: Re: [R] Merge the data from multiple text files
On 1/5/19 7:28 AM, Priya Arasu via R-help wrote:
> I have multiple text files, where each file has Boolean rules.
> Example of my text file 1 and 2
> Text file 1:
> A = not(B or C)
> B = A and C
> C = D
> Text file 2:
> A = D and E
> B = not(D)
>
> I want to merge the contents in text file as follows
> A = not(B or C) and (D and E)
> B = not(D) and (A and C)
> C = D
> Is there a code in R to merge the data from multiple text files?
There is a `merge` function. For this use case you would need to first
parse your expressions so that the LHS was in one character column and
the RHS was in another character column in each of 2 dataframes. Then
merge on the LHS columns and `paste` matching values from the two
columns. You will probably need to learn how to use `ifelse` and `is.na`.
> Thank you
> Priya
>
> [[alternative HTML version deleted]]
You also need to learn that R is a plain text mailing list and that each
mail client has its own method for building mail in plain text.
--
David.
>
> __
> R-help@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.
__
R-help@r-project.org mailing lis
[R] Merge the data from multiple text files
I have multiple text files, where each file has Boolean rules. Example of my text file 1 and 2 Text file 1: A = not(B or C) B = A and C C = D Text file 2: A = D and E B = not(D) I want to merge the contents in text file as follows A = not(B or C) and (D and E) B = not(D) and (A and C) C = D Is there a code in R to merge the data from multiple text files? Thank you Priya [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Function to save results
Hi David,Thank you for the example.When I try to use the cat function, I get an
error
cat(attr<-getAttractors(net, type="asynchronous"))Error in cat(attr <-
getAttractors(net, type = "asynchronous")) :
argument 1 (type 'pairlist') cannot be handled by 'cat'
Please let me know, if I have used the function in right way?.
Thank you
Priya
On Wednesday, 1 November 2017 9:32 PM, David L Carlson
wrote:
Let's try a simple example.
> # Create a script file of commands
> # Note we must print the results of quantile explicitly
> cat("x <- rnorm(50)\nprint(quantile(x))\nstem(x)\n", file="Test.R")
>
> # Test it by running it to the console
> source("Test.R")
0% 25% 50% 75% 100%
-2.4736219 -0.7915433 -0.1178056 0.7023577 2.9158617
The decimal point is at the |
-2 | 510
-1 | 7631110
-0 | 998877733211
0 | 011244889
1 | 00045
2 | 19
>
> # Now run it and save the file
> sink("Testout.txt")
> source("Test.R")
> sink()
>
> # What is located in "Testout.txt"?
> cat(readLines("Testout.txt"), sep="\n")
0% 25% 50% 75% 100%
-2.47511893 -0.47919111 0.05761628 0.67403447 1.79825459
The decimal point is at the |
-2 | 5
-2 | 4
-1 |
-1 | 432000
-0 | 87755
-0 | 442110
0 | 001244
0 | 556789
1 | 113
1 | 5788
> # Success
Depending on your operating system, you may also be able to save the output
with File | Save to File.
---
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Priya Arasu via
R-help
Sent: Wednesday, November 1, 2017 9:57 AM
To: Eric Berger
Cc: r-help@r-project.org
Subject: Re: [R] Function to save results
Hi Eric,Thanks for the explanation. Is there a way to save the results
automatically after the analysis gets over?. As I recently lost the results,
because I didn't save the results. I don't want to run the sink or save command
after the analysis is over rather run the command for saving the file before
starting to run the analysis, so the file gets saved automatically after the
script has finished running Priya
On Wednesday, 1 November 2017 7:53 PM, Eric Berger
wrote:
Hi Priya,
You did not follow the logic of the pseudo-code. The sink("filename"), sink()
pair captures whatever output is generated between the first sink statement and
the second sink statement.You need (possibly) to do:
sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//attr. txt") net <- loadNetwork("C://Users//Priya/
/Desktop//Attractor analysis_all genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")attr <- getAttractors(net, type="asynchronous")
sink()
HTH,Eric
Hi Eric,I tried as you suggested but I could not find the output in the text
file I created (attr.txt)
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")sink("C://Users//Priya// Desktop//Attractor
analysis_all genes//synaptogenesis//attr. txt")
sink()
attr <- getAttractors(net, type="asynchronous")
Priya
On Wednesday, 1 November 2017 6:54 PM, Eric Berger
wrote:
Some comments:1. sink() does not return a value. There is on point to set attr
<- sink(...). Just give the command sink("C://etc")2. to complete the
saving to the file you must give a second sink command with no argument:
sink()So your code would be (pseudo-code, not actual code) sink( "filename" )do
something that prints output which will be captured by sinksink() HTH,Eric
On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help
wrote:
Hi,I want the results to be saved automatically in a output text file after the
script has finished running.
I used the sink function in the following example, but the results file
(output.txt) was empty.
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")#
First I loaded theinput file for which I want to identify attractors attr <-
sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//output. txt")# used the sink function to save the
results from attr function
attr <- getAttractors(net, type="asynchronous")# then ran the script for
identifying attractors Is there any function to save the results before setting
the script to run, so that results are automatically saved in a text file after
the s
Re: [R] Function to save results
Hi Eric,Thanks for the explanation. Is there a way to save the results
automatically after the analysis gets over?. As I recently lost the results,
because I didn't save the results. I don't want to run the sink or save command
after the analysis is over rather run the command for saving the file before
starting to run the analysis, so the file gets saved automatically after the
script has finished running
Priya
On Wednesday, 1 November 2017 7:53 PM, Eric Berger
wrote:
Hi Priya,
You did not follow the logic of the pseudo-code. The sink("filename"), sink()
pair captures whatever output is generated between the first sink statement and
the second sink statement.You need (possibly) to do:
sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//attr. txt")
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")attr
<- getAttractors(net, type="asynchronous")
sink()
HTH,Eric
On Wed, Nov 1, 2017 at 4:10 PM, Priya Arasu wrote:
Hi Eric,I tried as you suggested but I could not find the output in the text
file I created (attr.txt)
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")sink("C://Users//Priya// Desktop//Attractor
analysis_all genes//synaptogenesis//attr. txt")
sink()
attr <- getAttractors(net, type="asynchronous")
Priya
On Wednesday, 1 November 2017 6:54 PM, Eric Berger
wrote:
Some comments:1. sink() does not return a value. There is on point to set attr
<- sink(...). Just give the command sink("C://etc")2. to complete the
saving to the file you must give a second sink command with no argument:
sink()So your code would be (pseudo-code, not actual code)
sink( "filename" )do something that prints output which will be captured by
sinksink()
HTH,Eric
On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help
wrote:
Hi,I want the results to be saved automatically in a output text file after the
script has finished running.
I used the sink function in the following example, but the results file
(output.txt) was empty.
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")#
First I loaded theinput file for which I want to identify attractors
attr <- sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//output. txt")# used the sink function to save the
results from attr function
attr <- getAttractors(net, type="asynchronous")# then ran the script for
identifying attractors
Is there any function to save the results before setting the script to run, so
that results are automatically saved in a text file after the script has
finished running?
Thank youPriya
[[alternative HTML version deleted]]
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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/ posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Function to save results
Hi Eric,I tried as you suggested but I could not find the output in the text
file I created (attr.txt)
net <- loadNetwork("C://Users//Priya//Desktop//Attractor analysis_all
genes//synaptogenesis//regulationof_dopamine_signaling_submodule3.txt")sink("C://Users//Priya//Desktop//Attractor
analysis_all genes//synaptogenesis//attr.txt")
sink()
attr <- getAttractors(net, type="asynchronous")
Priya
On Wednesday, 1 November 2017 6:54 PM, Eric Berger
wrote:
Some comments:1. sink() does not return a value. There is on point to set attr
<- sink(...). Just give the command sink("C://etc")2. to complete the
saving to the file you must give a second sink command with no argument:
sink()So your code would be (pseudo-code, not actual code)
sink( "filename" )do something that prints output which will be captured by
sinksink()
HTH,Eric
On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help
wrote:
Hi,I want the results to be saved automatically in a output text file after the
script has finished running.
I used the sink function in the following example, but the results file
(output.txt) was empty.
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")#
First I loaded theinput file for which I want to identify attractors
attr <- sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//output. txt")# used the sink function to save the
results from attr function
attr <- getAttractors(net, type="asynchronous")# then ran the script for
identifying attractors
Is there any function to save the results before setting the script to run, so
that results are automatically saved in a text file after the script has
finished running?
Thank youPriya
[[alternative HTML version deleted]]
__
R-help@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.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Function to save results
Hi,I want the results to be saved automatically in a output text file after the
script has finished running.
I used the sink function in the following example, but the results file
(output.txt) was empty.
net <- loadNetwork("C://Users//Priya//Desktop//Attractor analysis_all
genes//synaptogenesis//regulationof_dopamine_signaling_submodule3.txt")# First
I loaded theinput file for which I want to identify attractors
attr <- sink("C://Users//Priya//Desktop//Attractor analysis_all
genes//synaptogenesis//output.txt")# used the sink function to save the results
from attr function
attr <- getAttractors(net, type="asynchronous")# then ran the script for
identifying attractors
Is there any function to save the results before setting the script to run, so
that results are automatically saved in a text file after the script has
finished running?
Thank youPriya
[[alternative HTML version deleted]]
__
R-help@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.
[R] Help-Text file
Hi, I am using R 3.3.1 in R studio version 1.0.44 (Windows10, 64 bit system). I could import text file with Boolean rules, but when I start doing analysis in R, I get the error: I have been trying to do attractor analysis using R package Boolnet, using the command: attr <- getAttractors(net, type="asynchronous"). This command throws up the below error: Error in matrix(nrow = n, ncol = length(network$genes)) : invalid 'nrow' value (too large or NA) In addition: Warning message: In matrix(nrow = n, ncol = length(network$genes)) : NAs introduced by coercion to integer range Have anyone come across this error?. I have attached the text file with Boolean rules. Pls find it. Any suggestions or ideas, would be of great help Thank you Priya Targets, factors DISC1, (!miR124 & !let7b & !let7a & !let7d) | (PCM1 & BBS4) | (MITF | GATA1 | TAL1 | EZH2 | AR | TCF3 | HNF4A | RUNX1) MITF, (MITF) GATA1, (GATA1) TAL1, (!miR377) | (TAL1) EZH2, (!miR124) | (EZH2) AR, (!miR124) | (AR) TCF3, (!miR124) | (TCF3) miR124, (EGR1) miR377, (miR377) let7b, (let7b) let7a, (let7a) let7d, (let7d) PCM1, (! miR33a) | (DISC1 & BBS4) | (EGR1 | SALL4 | POU3F2 | THAP11 | HCFC1 | ZFP281 | WT1 | SOX2 | CUX1 | SIN3B | KDM5B | HOXB4 | ELK1 | TCF3 | FLI1 | HNF4A | RUNX1 | MITF) miR33a, (miR33a) EGR1, (! miR124) | (EGR1) SALL4, (SALL4) POU3F2, (POU3F2) THAP11, (THAP11) HCFC1, (HCFC1) ZFP281, (ZFP281) WT1, (WT1) SOX2, (SOX2) CUX1, (CUX1) SIN3B, (SIN3B) KDM5B, (KDM5B) HOXB4, (HOXB4) ELK1, (ELK1) FLI1, (FLI1) HNF4A, (HNF4A) RUNX1, (RUNX1) BBS4, (! miR432 & ! miR382 & ! miR127 & ! miR377) | (DISC1 & PCM1) | (E2F1 | GATA1 | FLI1 | MITF | ELK1 | CUX1 | KDM5B | SIN3B) | GABP | EOMES | TFAP2A) miR432, (miR432) miR382, (miR382) miR127, (miR127) E2F1, (! let7a) | (E2F1) TFAP2A, (TFAP2A) EOMES, (EOMES) GABP, (GABP) __ R-help@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.
[R] Stop R script from running, when the memory goes beyond 15.4GB
Hi, I am using R 3.3.1 in RedHat Linux7 , 64bit system (16GB RAM). I could run simulation in R package, Boolnet for 25 genes without any problem. When I add more gene i.e. 26 genes, the system becomes slow. Simulation keeps running for more than a day. I have to stop the simulation, as it takes a lot of memory. I need a suggestion here, I want to stop the script from running when the script takes memory beyond 15.4 GB. How do I do it? Should I generate warning in my script or use typeCatch? Any idea or advice, would be of great help Thank you Priya [[alternative HTML version deleted]] __ R-help@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.
