similar to: Conditional Counting with Table

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

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

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

Greetings, I am new to R, but trying to put in the time to learn. I have read the R manual and several other introductory texts; however, there is nothing like actually putting it into practice. So here is my problem, and its more of a learning exercise for myself than anything else, but I'm stuck and getting extremely frustrated that I can't figure it out. I'm trying to make a

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

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

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

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, 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

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

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”),

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

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 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

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

Hi everybody, I would like to know whether it is possible to compare to tables for certain parameters. I have these two tables: gene table name chr start end str accession Length gen1 4 646752 646838 + MI0005806 86 gen12 2L 243035 243141 - MI0005821 106 gen3 2L 159838 159928 + MI0005813 90 gen7 2L

Hello, I have an input file: http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt where col 1 is chromosome, column2 is start of region, column 3 is end of region, column 4 and 5 is base position, column 6 is total reads, column 7 is methylation data, and column 8 is the strand. I would like a summary output file such as:

Hi all, Suppose I have 2 matrices A and B. And I want to measure how good each of this matrix is. So I intend to compare A and B with another "gold standard" matrix X. Meaning the more similar a matrix to X the better it is. What is the common way in R to measure matrix similarity (ie. A vs X, and B vs X) ? - Gundala Viswanath Jakarta - Indonesia

Dear all, I tried to find index in repo given a query with this: > repo <- c("AAA", "AAT", "AAC", "AAG", "ATA", "ATT") > qr <- c("AAC", "ATT", "ATT") > which(repo%in%qr) [1] 3 6 Note that the query contain repeating elements, yet the output of which only returns unique. How can I make it