Question: problems in arrays
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gravatar for Brian Moldover
9.5 years ago by
Brian Moldover30 wrote:
Hello all, I'm trying to use the overlapper.R script to calculate Venn intersections between gene lists. Apparently there is a lot of user error, as I cannot get any output. Here is what I am doing. 1. Start R 2.9.0 2. Start the script: >source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scrip ts/ove rLapper.R") 3. Define the setlist: > setlist <- list(A=sample(letters, 2707), B=sample(letters, 3812), C=sample(letters, 1215), D=sample(letters, 943), E=sample(letters, 4320, replace=T)) 4. Copy the Excel data into the clipboard. 5. Read the data into R: > read.delim("clipboard", header=F) a. Sample input 4318 NA NA NA NA 7650653 4319 NA NA NA NA 7650725 4320 NA NA NA NA 7650735 6. Calculate the Venn overlaps: > OLlist <- overLapper(setlist=setlist, sep="", type="vennsets"); OLlist; names(OLlist) But the array data appears to be empty, since I can output a file but no overlaps between the sets. The export file has the possible overlaps, but no probeID's.Help? J - Brian [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.5 years ago by Thomas Girke1.7k • written 9.5 years ago by Brian Moldover30
Answer: problems in arrays
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gravatar for Thomas Girke
9.5 years ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k wrote:
Dear Brian, It seems that you are having problems with generating the sample set list object that is passed on to the overLapper()/vennPlot() functions. The example you are giving below generates an Error, and therefore the final step doesn't generate the expected result. To generate the test sample list with your command (3) you have to add 'replace=TRUE' to each sample() instance when you request more than 26 letters: source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Script s/overLapper.R") setlist <- list(A=sample(letters, 2707, replace=T), B=sample(letters, 3812, replace=T), C=sample(letters, 1215, replace=T), D=sample(letters, 943, replace=T), E=sample(letters, 4320, replace=T)) OLlist5 <- overLapper(setlist=setlist, sep="_", type="vennsets", keepdups=T) counts <- sapply(OLlist5$Venn_List, length) vennPlot(counts=counts, ccol=c(rep(1,30),2), lcex=1.5, ccex=c(rep(1.5,5), rep(0.6,25),1.5)) For more detailed information on my personal custom intersect/venn functions, please consult this page: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.htm l#R_graphics_venn To get your data into R from Excel, you can use the copy&paste approach, but this is a bit tedious. The best might be to set up your five sample sets in an Excel table with 5 columns, then you save it to a tab- delimited text file and import it into R with the read.delim() function: mytable <- read.delim(file="mytable") Once you have it in R, you can convert into a list with lapply(). Here is an example for the iris data set: setlist <- lapply(colnames(iris), function(x) as.character(iris[,x])) names(setlist) <- LETTERS[1:5] Alternatively, you could do this 'manually' like this: setlist <- list(A=as.character(mytable[,1]), B=as.character(mytable[,2]), C=as.character(mytable[,3]), D=as.character(mytable[,4]), E=as.character(mytable[,5])) I hope this helps. Thomas On Wed, Oct 14, 2009 at 12:14:34PM -0400, Brian Moldover wrote: > Hello all, I'm trying to use the overlapper.R script to calculate Venn > intersections between gene lists. Apparently there is a lot of user error, > as I cannot get any output. Here is what I am doing. > > > > 1. Start R 2.9.0 > > 2. Start the script: > >source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scr ipts/ove > rLapper.R") > > 3. Define the setlist: > setlist <- list(A=sample(letters, 2707), > B=sample(letters, 3812), C=sample(letters, 1215), D=sample(letters, 943), > E=sample(letters, 4320, replace=T)) > > 4. Copy the Excel data into the clipboard. > > 5. Read the data into R: > read.delim("clipboard", header=F) > > a. Sample input > > 4318 NA NA NA NA 7650653 > > 4319 NA NA NA NA 7650725 > > 4320 NA NA NA NA 7650735 > > > > 6. Calculate the Venn overlaps: > OLlist <- > overLapper(setlist=setlist, sep="", type="vennsets"); OLlist; names(OLlist) > > > > But the array data appears to be empty, since I can output a file but no > overlaps between the sets. The export file has the possible overlaps, but no > probeID's.Help? J > > > > > > > > - Brian > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 9.5 years ago by Thomas Girke1.7k
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