search for: chr3

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: browser position chr1:1-10000 browser hide all track type=wiggle_0 name=sample description=chr1_sample visibility=full variableStep chrom=chr1 span=1 and then insert 2 lines before each chromoso...

..." 77 78 1 "chr2" 80 81 4 "chr2" 85 86 0 "chr2" 99 100 1 "chr2" 105 106 0 "chr2" 120 121 1 "chr2" 130 131 1 "chr2" 140 141 0 "chr2" 150 151 5 "chr3" 172 173 0 "chr3" 177 178 1 "chr3" 190 191 6 "chr3" 200 201 8 "chr3" 220 221 0 "chr3" 300 301 9 "chr3" 310 311 10 --------------------------------- tb2< v1 v2 v3 "chr...

...Ref Alt Func.refGene Gene.refGene 284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194 465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910 525 chr2 223777758 223777758 T A exonic AP1S3 626 chr3 99794575 99794575 G A exonic COL8A1 643 chr3 132601066 132601066 A G exonic ACKR4 655 chr3 132601999 132601999 A G exonic BCDF5,CDFG6", header=TRUE,stringsAsFactors=FALSE) df.sample.out <- ( df.sample.gene %>% mutate( Gene.ref...

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 add a new column with the count number; the new data frame should look like thi...

...efGene Gene.refGene284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910525 chr2 223777758 223777758 T A exonic AP1S3626 chr3 99794575 99794575 G A exonic COL8A1643 chr3 132601066 132601066 A G exonic ACKR4 How could I obtain a dataframe where each line that has multiple gene names (in the field Gene.refGene) is replicated with only one gene name ? i.e. for the secon...

...End Ref Alt Func.refGene Gene.refGene 284 chr2 16080996 16080996 C T ncRNA_exonic GACAT3 448 chr2 113979920 113979920 C T ncRNA_exonic LINC01191,LOC100499194 465 chr2 131279347 131279347 C G ncRNA_exonic LOC440910 525 chr2 223777758 223777758 T A exonic AP1S3 626 chr3 99794575 99794575 G A exonic COL8A1 643 chr3 132601066 132601066 A G exonic ACKR4 655 chr3 132601999 132601999 A G exonic BCDF5,CDFG6", header=TRUE,stringsAsFactors=FALSE) multgenes<-grep(",",df.sample.gene$Gene.refGene) rep_genes<-strspli...

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...

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 to obtain the format I want df1=read.table("df1.tx...

...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 100 100 CHH 0 0.0 + 6 chr4 450 450 CG 0 0.0 + 7 chr5 450 450 CHH 0 0.0 + 8 chr5 50034 50034 CHG 0 0.0 + 9 chr7 50055 50055 CHG 0 0.0 + 10 chr10 50063 50063 CHH 0 0.0 + > dput(data) structure(list(V1 = structure(c(1L, 1L, 3L, 3L, 4L, 5L, 6L, 6L, 7L, 2L), .Label...

...ucture(list(chrom = structure(c(3L, 3L, 3L, 3L, 3L, 3L), .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrX"), class = "factor"), start = c(5291000L, 10988025L, 11767950L, 11840900L, 12267450L, 12276675L), end = c(5291926L, 10988526L, 11768676L, 11841851L, 12268076L...

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 lexicographically in my figure ( chr1 > chr10 > chr11 > ... ) ? this is correct. However, the code I use to draw lines between points in the xyplot connects points i...

...else, but I'm stuck and getting extremely frustrated that I can't figure it out. I'm trying to make a fairly simple figure, but also trying to make it look "better" using ggplot2. I have data.frame that contains chrom length 1 chr1 249250621 2 chr2 243199373 3 chr3 198022430 4 chr4 191154276 5 chr5 180915260 6 chr6 171115067 7 chr7 159138663 8 chrX 155270560 9 chr8 146364022 10 chr9 141213431 11 chr10 135534747 12 chr11 135006516 13 chr12 133851895 14 chr13 115169878 15 chr14 107349540 16 chr15 102531392 17 chr16 90354753 18 chr17...

...{BC062579} \code{BC063107} \code{BC063682} \code{BC066360} \code{BT007082} \code{BT007136} \code{BT007305} \code{BX537637} \code{J02969} \code{M37712} \code{M83653} \code{NM_003327} \code{X04526} \code{X75962} \code{Y16846}} \item{\code{chrom}}{a factor with levels \code{chr1} \code{chr2} \code{chr3}} \item{\code{strand}}{a factor with levels \code{-} \code{+}} \item{\code{txStart}}{a numeric vector} \item{\code{txEnd}}{a numeric vector} } } \usage{data(KG)} \format{data frame} \source{The UCSC genome browser (http://genome.ucsc.edu).} \keyword{datasets} PACKAGE/man/Einter.Rd: \...

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= ) >chr1=MEDIPS.genomeVector(data=chr1, bin_size=50,extend=250) ... ... >write.table(frameschr1.frame500.step250, file="frames.chr1.meth.txt&qu...

...DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD") # 100bp C free sequence query.plus <- DNAString("DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD") # 60bp C free sequence query.minus <- reverseComplement(query.plus) chrList <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19&q...

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:

SUMMARY: -------- I tried to identify the general and root causes for these problems with 1.9, by taking into account non-utf encoding, current patches, comments and ideas. I used ticket #2188 as base for explanations. This is a long read. I wanted to include all the relevant information in one place. I also included information about related tickets in LH and their status. I decided that adding