similar to: dispatch on "c" method when passing named arguments

Hi Peter I have the following data frame with chromosome name, start and end positions: chrN start end 1 chr1 11122333 11122633 2 chr1 11122333 11122633 3 chr3 11122333 11122633 8 chr3 111273334 111273634 7 chr2 12122334 12122634 4 chr1 21122377 21122677 5 chr2 33122355 33122655 6 chr2 33122355 33122655 I would like to count the positions that have the same start and

Hello, I'm a new R user. I have two different dummy tables with the variable name tb1 and tb2. tb1< v1 v2 v3 v4 "chr1" 22 23 3 "chr1" 36 37 1 "chr1" 54 55 0 "chr1" 77 78 1 "chr2" 80 81 4 "chr2" 85 86 0 "chr2" 99 100 1

Hi Jim I am trying to prepare a bed file to load as accustom track on the UCSC genome browser. I have a data frame that looks like the one below. > x V1 V2 V3 1 chr1 11255 55 2 chr1 11320 29 3 chr1 11400 45 4 chr2 21680 35 5 chr2 21750 84 6 chr2 21820 29 7 chr2 31890 46 8 chr3 32100 29 9 chr3 52380 29 10 chr3 66450 46 I would like to insert the following 4 lines at the beginning:

Hello, I have an R script that I use as a template to perform a task for multiple files (in this case, multiple chromosomes). What I would like to do is to utilize a simple loop to parse through each chromosome number so that I don't have to type the same code over and over again in the R console. I've tried using: for(i in 1:22){ etc.. } and replacing each chromosome number with

Hello, Everyone, how to use "loop" to make the process automatic and fast? When compute each sample, the script type in R almost the same, just the input and output file's name is changed(chr1 change to chr2, chr3,chr4...). The first sample's script like this: >chr1=MEDIPS.readAlignedSeqences(BSgenome="hg19", file="chr1",numrows= )

Hello I have 2 data frames df1 and df2. I would like to create a new data frame new_df which will contain only the common rows based on the first 2 columns (chrN and start). The column score in the new data frame should be replaced with a column containing the average score (average_score) from df1 and df2. df1= data.frame(chrN= c(“chr1”, “chr1”, “chr1”, “chr1”, “chr2”, “chr2”, “chr2”),

I have a dataframe in the general format: chr1 0.5 chr1 0 chr1 0.75 chr2 0 chr2 0 chr3 1 chr3 1 chr3 0.5 chr7 0.75 chr9 1 chr9 1 chr22 0.5 chr22 0.5 where the first column is the chromosome location and the second column is some value. What I'd like to do is have a histogram created for each chr location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and chr22). I am just

Hi, I am given the following table: > head(hsa_refseq) chr genome region start stop nu strand nu.1 nu.2 gene_id 1 chr1 hg19_refGene CDS 67000042 67000051 0 + 0 gene_id NM_032291 2 chr1 hg19_refGene exon 66999825 67000051 0 + . gene_id NM_032291 3 chr1 hg19_refGene CDS 67091530 67091593 0 + 2 gene_id NM_032291 4 chr1 hg19_refGene exon

Hello,   I have a dataframe: dd <- data.frame(b = c("chr2", "chr1", "chr15", "chr13"),         x = c("A", "D", "A", "C"), y = c(8, 3, 9, 9),         z = c(1, 1, 1, 2))   >dd       b x y z 1  chr2 A 8 1 2  chr1 D 3 1 3 chr15 A 9 1 4 chr13 C 9 2 Now I want to sort them according column "b", but only its

I've been looking for how to change a certain percentage of values in a data frame, but I've been struggling to find information in R. For example: #################example data############## > data V1 V2 V3 V4 V5 V6 V7 1 chr1 500 500 CHH 0 0.5 + 2 chr1 550 550 CHH 0 0.0 + 3 chr2 700 700 CHH 0 0.0 + 4 chr2 1000 1000 CHH 0 0.0 + 5 chr3

Hi R experts. how can I average two sets of columns? dd <- data.frame(b = c("chr2", "chr1", "chrY", "chr13", "chrX"),         w=11:15, x = 1:5, y = c(8, 3, 9, 9,7),        z = c(1, 1, 1, 2, 8)) expected result for mean(w,x) and mean(y,z) is 1  chr2 6  4.5 2  chr1 7  2 3  chrY 8  5 4 chr13 9  5.5 5  chrX 10 7.5 Yu [[alternative

I have the following xyplot figure: http://img577.imageshack.us/img577/686/filesizeresults12000000.png The data are organized in a matrix file as follows: Type Elements Chromosome Time bedGz 12000000 chr1 14.240 bedGz 12000000 chr2 7.949 bedGz 12000000 chr3 5.103 bedGz 12000000 chr4 5.290 bedGz 12000000 chr5 5.161 ... The x-axis labels in the Chromosome column are ordered

I want to remove the column names from a data frame. I do it the long way, can any body show me a better way ? df= data.frame(chrN= c(“chr1”, “chr2”, “chr3”), start= c(1, 2, 3), end= c(4, 5, 6), score= c(7, 8, 9)) df #I write a txt file without row or column names write.table(df,"df1.txt",sep='\t',quote=FALSE,row.names=F,col.names=F) #then I read it with the header = F

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Dear all, I have the following data frame: V1 V2 aaa chr1 aaa chr2 aaa NM aaa QC aaa chr10 att NM att chr7 What I want to do is to count the string (V1). But the condition of counting is: if the V2 of the string is "NM" or "QC" then the count is not increased. Hence the contigency table will look like this: #tag count aaa 3 att 1 Is

Hello all, I have written a for loop to act on a dataframe with close to 3million rows and 6 columns and I would like to pass it to apply() to speed the process up (I let the loop run for 2 days before stopping it and it had only gone through 200,000 rows) but I am really struggling to find a way to pass the arguments. Below are the loop and the head of the dataframe I am working on. Any hints

This is due to the intentional truncation of ANY suffixes from method signatures. I've hacked selectMethod() to be robust to that and will commit soon. Thanks for the report. Michael On Thu, Mar 14, 2019 at 9:32 AM Pages, Herve <hpages at fredhutch.org> wrote: > Here is an example: > > setGeneric("foo", function(x, y) standardGeneric("foo")) > >

If we started over, I'd try to avoid this sort of complexity, but "ANY" truncation has been happening since at least 2003. > matchSignature(c("numeric", "ANY"), foo) x "numeric" So I'm not sure we want to mess with it. Michael On Thu, Mar 21, 2019 at 8:14 PM Pages, Herve <hpages at fredhutch.org> wrote: > Hi Michael, >

Dear list, I wish to plot chromatin precipitation data: I would like to have a rectangles (x:end-start, y:peak) but I do not have an idea how to define x (in terms of qplot syntax) and to choose the correct geom. mydata is a subset of a larger file. > mydata chrom start end peak 1 chr11 5291000 5291926 8 2 chr11 10988025 10988526 7 3 chr11 11767950 11768676 8 4

Agreed but I'm not sure we want users accessing documentation with those types of aliases. One option is the method?foo("numeric") syntax. On Thu, Mar 21, 2019 at 9:52 PM Pages, Herve <hpages at fredhutch.org> wrote: > Fine with me as long as eliminating the inconveniences associated with it > can be put on the roadmap. The alias instability and the fact that the user