Displaying 5 results from an estimated 5 matches for "chr8".
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2008 Oct 06
2
Problem with Grep Under Loop
Dear all,
I have no problem with this individual grep command:
> datk <- grep("XM_528056", source$V1)
> dat2 <- source[datk,]
> print(dat2)
V1 V2 V3 V4 V5 V6 V7
35995 XM_528056 panTro2 chr8 + 1775569 1896107 Chimpanzee
BUT, when I run them under the loop it gives this error:
> hm_acc <- c("XM_528056","AB002296")
> for (i in 1:length(hm_acc)){
+
+ hm_acc_id <- as.character(hm_acc[i])
+ print(hm_acc_id)
+
+ hm_allk <- grep(hm_acc_id,sourc...
2010 May 14
1
finding the plot limits generated by default
I have two datasets that I would like to plot in a single figure. The first
plot is generated by a function that then takes a subset of the data. (It
is biological data so it is usually by chromosome e.g.
function(data1,subset="chr8") ) Since not only are the chromosomes different
sizes, but across different datasets there may be different numbers of
points for a single chromosome, I do not know the coordinates on the x-axis
prior to running the function.
I want the scale of the second plot to align to that of the first,...
2012 Sep 15
2
qplot: plotting precipitation data
...t;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, 12277051L), peak = c(8L,
7L, 8L, 8L, 12L, 7L)), .Names = c("chrom", "star...
2012 Jun 21
2
Simple Question?
...y 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 81195210
19 chr18 78077248
20 chr20 63025520
21 chrY 59373566
22 chr19 59128983
23 chr22 51304566
24 chr21...
2011 Apr 15
1
Whole genome searching of 100bp "D" sequence
...ring("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", "chr20", "chr21", "chr22", "chrX", "chr...