search for: chr15

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 n...

Hello I have a data frame and one of its columns is as follows: Col chr1:71310034 chr14:23354088 chr15:37759058 chr22:18262638 chrUn:31337214 chr10_random:4369261 chrUn:3545097 I would like to get rid of colon (:) and replace this column with two new columns containing the terms on each side of the colon. The new columns should look as follows: Col_a Col_b chr1 71310034 c...

...in parts of the file. For instance, from this text file: =================================================== Matches For Query 0 (108 bases): 000019_0070 =================================================== Score Q_Name S_Name Q_Start Q_End S_Start S_End Direction Bases identity 89 000019_0070 Chr15 3 108 43251883 43251778 C 106 95.28 88 000019_0070 Chr1 4 108 85826948 85826844 C 105 95.24 =================================================== Matches For Query 1 (124 bases): 000024_1262 =================================================== Score Q_Name S_Name Q_Start Q_End S_Start S_End Dir...

I have a data.frame with all character columns, I would like to convert the last two columns into numeric.> x[1:5, ] chrN start end 1 chr1 71310034 71310064 2 chr14 23354088 23354118 3 chr14 71310034 71310064 4 chr15 37759058 37759088 5 chr22 18262638 18262668 > apply(x, 2, FUN = mode) chrN start end "character" "character" "character" ____________________________________________________________________________________ Be a better friend, news...

...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", "chr9", "chrX"), class = "factor"), start = c(5291000L, 1098...

...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 "chr" and order the chrom column in ascending order with X & Y at the end. I have tried conve...

...lement(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 of annotation annotGr <- exons(txdb) #annotGr <- cds(txdb) wholeGenomeMatch <- funct...