Displaying 9 results from an estimated 9 matches similar to: "Read file line by line"
2018 Mar 12
0
Package gamlss used inside foreach() and %dopar% fails to find an object
Hello Mikis:
Thanks a lot, it worked. Could you tell me what the problem was?
Regards,
Nik
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2018 Mar 10
1
error message from sqldf
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
2011 Oct 19
1
replacing percentage of values in data frame
I've been looking for how to change a certain percentage of values in a data
frame, but 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
2008 Dec 24
1
Conditional Counting with Table
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
2010 Nov 07
1
How do I order xyplot line points?
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
2012 Sep 15
2
qplot: plotting precipitation data
Dear list,
I wish to plot chromatin precipitation data: I would like to have a
rectangles (x:end-start, y:peak) but I do not have an idea how to define x
(in terms of qplot syntax) and to choose the correct geom.
mydata is a subset of a larger file.
> mydata
chrom start end peak
1 chr11 5291000 5291926 8
2 chr11 10988025 10988526 7
3 chr11 11767950 11768676 8
4
2012 Jun 21
2
Simple Question?
Greetings,
I am new to R, but trying to put in the time to learn. I have read the R
manual and several other introductory texts; however, there is nothing like
actually putting it into practice. So here is my problem, and its more of a
learning exercise for myself than anything else, but I'm stuck and getting
extremely frustrated that I can't figure it out.
I'm trying to make a
2011 Apr 15
1
Whole genome searching of 100bp "D" sequence
Hi,
I was wondering I'm going about this in the correct way. I need to test if
there are coding sequences or exons in hg19 which match a string of 100bp
"D" i.e. [A,G or T]. However I'm getting a strange result.
I get a hit on chr7, using the 100bp search however when I search with 60bp
sequence of "D" I don't get any hits.
library("BSgenome")
2009 Mar 04
5
Filtering R lists
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