Hi,
I have taken Mr.Jeff's suggestions in producing a reproducible example and
edited my question again. Kindly someone in the mailing list, help to solve the
problem, which I have mentioned in the below mail
Thank youPriya
Dear Mr. Jeff Newmiller,
Thank you. I have gone through the
links that you have sent me to produce reproducible example. I will try to
explain the problem clearly this time.
I have been using Boolnet package, to simulate interaction between certain
genes. I have a problem after importing the text file (New_Text_Document_1) in
R and start doing the attractor analysis in Boolnet. I have pasted the steps
below, when I give the command "getAttractors" for doing attractor analysis, I
get the error (highlighted red and italicized).
> library("BoolNet", lib.loc="~/R/win-library/3.3")
> library(readr)#Imported txt file
> New_Text_Document_1 <- read_csv("C:/Users/Priya/Desktop/New Text
> Document-1.txt")
Parsed with column specification:
cols(
Targets = col_character(),
factors = col_character()
)
> View(New_Text_Document_1)
> net <- loadNetwork("C:/Users/Priya/Desktop/New Text Document-1.txt") #loaded
> the txt file as network (net) for analysis
> attr <- getAttractors(net, type="asynchronous") # attractor analysis for the
> txt file
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
Using dput, I have pasted the data (New_Text_Document_1), which I
have imported for doing attractor analysis.I have also attached the
New_Text_Document_1 along with this mail. I didn't get any reply from the
publishers of Boolnet package, so Kindly help. Have anyone come across this
error and how do I fix this problem?
dput(New_Text_Document_1)
New_Text_Document_1 <- structure(list(Targets = c("DISC1", "MITF", "GATA1",
"TAL1", "EZH2", "AR", "TCF3", "miR124", "miR377", "let7b", "let7a", "let7d",
"PCM1", "miR33a", "EGR1", "SALL4", "POU3F2", "THAP11", "HCFC1","ZFP281", "WT1",
"SOX2", "CUX1", "SIN3B", "KDM5B", "HOXB4", "ELK1", "FLI1", "HNF4A", "RUNX1",
"BBS4", "miR432", "miR382", "miR127", "E2F1", "TFAP2A", "EOMES", "GABP"),
factors = c("(!miR124 & !let7b & !let7a & !let7d) | (PCM1 & BBS4) | (MITF |
GATA1 | TAL1 | EZH2 | AR | TCF3 | HNF4A | RUNX1)",
"(MITF)", "(GATA1)", "(!miR377) | (TAL1)", "(!miR124) | (EZH2)",
"(!miR124) | (AR)", "(!miR124) | (TCF3)", "(EGR1)", "(miR377)",
"(let7b)", "(let7a)", "(let7d)", "(! miR33a) | (DISC1 & BBS4) | (EGR1 | SALL4 |
POU3F2 | THAP11 | HCFC1 | ZFP281 | WT1 | SOX2 | CUX1 | SIN3B | KDM5B | HOXB4 |
ELK1 | TCF3 | FLI1 | HNF4A | RUNX1 | MITF)", "(miR33a)", "(! miR124) | (EGR1)",
"(SALL4)", "(POU3F2)", "(THAP11)","(HCFC1)", "(ZFP281)", "(WT1)", "(SOX2)",
"(CUX1)", "(SIN3B)",
"(KDM5B)", "(HOXB4)", "(ELK1)", "(FLI1)", "(HNF4A)", "(RUNX1)",
"(! miR432 & ! miR382 & ! miR127 & ! miR377) | (DISC1 & PCM1) | (E2F1 | GATA1 |
FLI1 | MITF | ELK1 | CUX1 | KDM5B | SIN3B) | GABP | EOMES | TFAP2A)",
"(miR432)", "(miR382)", "(miR127)", "(! let7a) | (E2F1)", "(TFAP2A)",
"(EOMES)", "(GABP)")),
class = c("tbl_df", "tbl", "data.frame"),
row.names = c(NA, -38L), .
Names = c("Targets", "factors"),
spec = structure(list(cols = structure(list(Targets = structure(list(), class =
c("collector_character","collector")),
factors = structure(list(), class = c("collector_character", "collector"))), .
Names = c("Targets", "factors")),
default = structure(list(),
class = c("collector_guess", "collector"))), .
Names = c("cols", "default"), class = "col_spec"))
Regards
Priya
On Saturday, 5 November 2016 10:28 PM, Jeff Newmiller
<jdnew...@dcn.davis.ca.us> wrote:
Sorry, but this request is quite hard to understand... you are basically
directing your question at an incredibly narrow set of people who happen to
have combined your kind of data read in the way you read it in with your kind
of analysis algorithms while telling us almost nothing about how you did those
things.
Please read the Posting Guide mentioned in the footer of every posting on this
list and provide a reproducible example [1][2]. If the problem is in your use
of R then someone here will be able to help. If your problem is inside a
contributed package then you may need the assistance of the package maintainer,
but they will also need a reproducible example so your effort will not be in
vain. Also, the act of creating a RE often leads you to your own solution even
without getting outside help.
[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
[2] http://adv-r.had.co.nz/Reproducibility.html
--
Sent from my phone. Please excuse my brevity.
On November 4, 2016 10:28:48 PM PDT, Priya Arasu via R-help
<r-help@r-project.org> wrote:
>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
>
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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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