search for: chr1

Hi all, I am given the a data frame in which one of the columns has more information together- see column 4, peak_loc: chr start end peak_loc cluster_TC strand peak_TC 1 chr1 564620 564649 chr1:564644..564645,+ 94 + 10 2 chr1 565369 565404 chr1:565371..565372,+ 217 + 8 3 chr1 565463 565541 chr1:565480..565481,+ 1214 + 15 4 chr1 565653 565697 chr1:565662..565663,+ 1031 + 28 5 chr1 565861 565922 chr1:5658...

Hi,? I have two big data set.? data _1 :? > dim(data_1) [1] 15820 5 > head(data_1) ? ?Chromosome ?????Start????????End????????Feature GroupA_3 1: ? ? ? ????????chr1 521369 ?750000 ????chr1-0001 ? ?????0.170 2: ? ? ? ????????chr1 750001 ?800000 ????chr1-0002 ? ????-0.086 3: ? ? ? ????????chr1 800001 ?850000 ????chr1-0003 ? ?????0.006 4: ? ? ? ????????chr1 850001 ?900000 ????chr1-0004 ? ?????0.050 5: ? ? ? ????????chr1 900001 ?950000 ????chr1-0005 ? ?????0.062 6...

Hi all, I read in a column which looks like "chr1:000889594-000889638", and need to break them into three columns like "chr1:", "000889594" and "000889638". How shall I do in R. Thanks a lot for your suggestions! Bill

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 des...

...tly? Longer: Here's more info: * The data.frame itself ~ 15.8 MB when loaded. * ~ 400,000 rows, 8 columns It looks like so: exon.start exon.width exon.width.unique exon.anno counts symbol transcript chr 1 4225 468 0 utr 0 WASH5P WASH5P chr1 2 4833 69 0 utr 1 WASH5P WASH5P chr1 3 5659 152 38 utr 1 WASH5P WASH5P chr1 4 6470 159 0 utr 0 WASH5P WASH5P chr1 5 6721 198 0...

Hello I have a data frame as below V1 V2 V3 V4 V5 V6 chr1 18884 C CAAAA 2 0 chr1 135419 TATACA T 2 0 chr1 332045 T TTG 0 2 chr1 453838 T TAC 2 0 chr1 567652 T TG 1 0 chr1 602541 TTTA T 2 0 on which I want to perform complex rearrangement such that: if V3 is a string >1 (i.e l...

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...

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&qu...

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow: chr1: 100-150 chr1: 300-350 I have thousands of these regions (some overlap and some not). Regards, --Yadav [[alternative HTML version deleted]]

Hi all, I have a column that has the following format: chr1:564588..564589,+ and I want to extract only the coordinates; I have tried writing a regular expression but I couldn't figure out how I should write it. Does anyone know? Thank you, Best, Nanami [[alternative HTML version deleted]]

HI, Try this: dat1<- read.table(text=" ?V1,V2,V3,V4,V5,V6,V7 ?chr1,564563,564598,564588 564589,1336,+,134 ?chr1,564620,564649,564644 564645,94,+,10 ?chr1,565369,565404,565371 565372,217,+,8 ?chr1,565463,565541,565480 565481,1214,+,15 ?chr1,565653,565697,565662 565663,1031,+,28 ?chr1,565861,565922,565883 565884,316,+,12 ",sep=",",header=TRUE,stringsA...

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 "chr2" 105 106 0 "chr2" 120 121 1...

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 67091530 67091593 0 + . gene_id NM_0...

...) } else if (all.tf7[i,1]!=all.tf7[i-1,1]) { all.tf7[i,6]<-(all.tf7[i-1,6]+1) x<-as.numeric(all.tf7[i,2]) } } #the aim here is to attribute a bin number to each row so that I can then split the dataframe according to those bins. chrom chromStart chromEnd name cumsum bin chr1 10089 10309 ZBTB33 10089 1 chr1 10132 10536 TAF7_(SQ-8) 20221 1 chr1 10133 10362 Pol2-4H8 30354 1 chr1 10148 10418 MafF_(M8194) 40502 1 chr1 10382 10578 ZBT...

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

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5 chr1 30 40 11 + I just wondering is there an efficient way to find overlapped, upstream and downstream genes for each gene in the grang...

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1 miRNA 1103243 1103332 + ACC="MI0000737"; ID="hsa-mir-200a"; exon 1103243 1103332 NR_029834 NR_029834 3 chr1 miRNA 11043...

...or a "-". In R-2.6.2patched (and every past version I have used) I never had problems in reading them in, as for example: > a <- read.table("coords.bed", skip=1) > disp(a) class data.frame dimensions are 38650 6 first rows: V1 V2 V3 V4 V5 V6 1 chr1 100088396 100088446 seq1 0 + 2 chr1 100088764 100088814 seq2 0 - If I do exactly the same command on the same file in R-2.7.0 the result I obtain is: > a <- read.table("coords.bed", skip=1) > disp(a) class data.frame dimensions are 38650 6 first rows: V1 V2...

...re slower and also require more memory than gzip. Bioconductor has big data packages and sometimes it makes sense to use gzip and not bzip2 or xz. For example, when loading Human chromosome 1 from disk, bzip2 and xz are 7 and 3.4 times slower than gzip, respectively: > system.time(load("chr1-gzip.rda")) user system elapsed 1.210 0.180 1.384 > system.time(load("chr1-bzip2.rda")) user system elapsed 9.500 0.160 9.674 > system.time(load("chr1-xz.rda")) user system elapsed 4.46 0.20 4.69 hpages at la...

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...