search for: chr10

Dear R users, I got the following error message from running sqldf code in R. do you know how to fix it? I read the sqldf package instruction and did not find a solution. Thank you, Ding chr10 <- sqldf("select * from manifest where CHR==10") UCN3cpg <- sqldf("select * from chr10 where MAPINFO between 5405573 and 5407594), overwrite = TRUE") Error: Table chr10 exists in database, and both overwrite and append are FALSE > ------------------------------...

...r message from sqldf Message-ID: coh.org> Content-Type: text/plain; charset="utf-8" Dear R users, I got the following error message from running sqldf code in R. do you know how to fix it? I read the sqldf package instruction and did not find a solution. Thank you, Ding chr10 <- sqldf("select * from manifest where CHR==10") UCN3cpg <- sqldf("select * from chr10 where MAPINFO between 5405573 and 5407594), overwrite = TRUE") Error: Table chr10 exists in database, and both overwrite and append are FALSE > ------------------------------...

Hi I got a file that looks like this: (i have shorten it alot the real file is over 200k rows long) chr10 rs7909677 101955 A G 0 1 0 1 0 0... chr10 rs2436025 238506 C G 1 0 0 1 0 0... chr10 rs11253562 148946 C T 0 1 0 0 1 ... chr10 rs1105116 230788 G T 0 0 1 0 0 1... chr10 rs4881551 149076 A G 0 1 0 0 1 0 0 1... What I want it to go trough the file and get the highest value in the third column so to s...

...00 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 = c("chr1", "chr10", "chr2", "chr3", "chr4", "chr5", "chr7"), class = "factor"), V2 = c(500L,...

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 there a co...

...1 chr11 5291000 5291926 8 2 chr11 10988025 10988526 7 3 chr11 11767950 11768676 8 4 chr11 11840900 11841851 8 5 chr11 12267450 12268076 12 6 chr11 12276675 12277051 7 > dput(mydata) structure(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&qu...

...rix 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 in numerical order ( chr1 > chr2 > ... ) ? this is incorrect. The problem this causes is most evident in the line that is drawn for the blue "bedGz" categor...

...e 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 81195210 19 chr18 78077248 20 chr20 63025520 21 chrY 59373566 22 chr19 59128983 23 chr22 51304566 24 chr21 48129895 I want to drop the "ch...

Hello I am am new to R and any help with the following would be appreciated: I have a list (example attached) and I would like to create a new list which is a filtered version of this list. I.e I would like a list that only contains elements with this value: Chr 10 : 21853562 - 21855482 Any pointers/tips would be great. Thanks! Nikol -- Bioinformatician/Computer Associate Cambridge Institute

...DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD") # 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", "chr20", "chr21", "chr22", "chrX", "chrY") #access/group the by subset...